diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6346287ac..2f4646244 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -54,7 +54,6 @@ jobs: - "latest-everything" nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: - - "conda" - "docker" - "singularity" isMaster: @@ -62,29 +61,9 @@ jobs: # Exclude conda and singularity on dev exclude: - isMaster: false - profile: "conda" - - isMaster: false profile: "singularity" - - profile: "conda" - nf_test_files: "tests/default.nf.test" - - profile: "conda" - nf_test_files: "tests/featurecounts_group_type.nf.test" - - profile: "conda" - nf_test_files: "tests/hisat2.nf.test" - - profile: "conda" - nf_test_files: "tests/kallisto.nf.test" - - profile: "conda" - nf_test_files: "tests/min_mapped_reads.nf.test" - - profile: "conda" - nf_test_files: "tests/remove_ribo_rna.nf.test" - - profile: "conda" - nf_test_files: "tests/salmon.nf.test" - - profile: "conda" - nf_test_files: "tests/skip_qc.nf.test" - - profile: "conda" - nf_test_files: "tests/skip_trimming.nf.test" - - profile: "conda" - nf_test_files: "tests/star_rsem.nf.test" + - NXF_VER: "latest-everything" + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 @@ -104,21 +83,6 @@ jobs: mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda - - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - name: Install nf-test uses: nf-core/setup-nf-test@v1 with: diff --git a/CHANGELOG.md b/CHANGELOG.md index fe18aecee..39e77a767 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,60 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [[3.17.0](https://github.com/nf-core/rnaseq/releases/tag/3.17.0)] - 2024-10-23 + +### Credits + +Special thanks to the following for their contributions to the release: + +- [Maxime Garcia](https://github.com/maxulysse) +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Pablo Gonzalez de Aledo](https://github.com/pabloaledo) + +### Enhancements & fixes + +- [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release +- [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have ARM builds +- [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build +- [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility +- [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility +- [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release +- [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers +- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies +- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix +- [PR #1440](https://github.com/nf-core/rnaseq/pull/1440) - Further reduce matrix +- [PR #1441](https://github.com/nf-core/rnaseq/pull/1441) - Force some containers to be converted from docker to singularity to fix nf-core download tests + +### Software dependencies + +| Dependency | Old version | New version | +| ----------------------------- | ----------- | ----------- | +| `bbmap` | 39.01 | 39.10 | +| `coreutils` | 8.30 | 9.5 | +| `fq` | 0.9.1 | 0.12.0 | +| `python (catadditionalfasta)` | 3.9.5 | 3.12.2 | +| `python (tx2gene)` | 3.9.5 | 3.10.4 | +| `cutadapt` | 3.4 | 4.9 | +| `htslib (star)` | 1.18 | 1.20 | +| `htslib` | 1.20 | 1.21 | +| `kallisto` | 0.48.0 | 0.51.1 | +| `preseq` | 3.1.2 | 3.2.0 | +| `salmon` | 1.10.1 | 1.10.3 | +| `samtools (star)` | 1.18 | 1.20 | +| `samtools` | 1.20 | 1.21 | +| `sortmerna` | 4.3.6 | 4.3.7 | +| `star` | 2.7.10a | =2.7.11b | +| `stringtie` | 2.2.1 | 2.2.3 | +| `subread` | 2.0.1 | 2.0.6 | +| `trim-galore` | 0.6.7 | 0.6.10 | +| `ucsc-bedgraphtobigwig` | 445 | 469 | + +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. + ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 ### Credits diff --git a/conf/arm.config b/conf/arm.config new file mode 100644 index 000000000..275af8c99 --- /dev/null +++ b/conf/arm.config @@ -0,0 +1,274 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running the pipeline with ARM architecture +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines custom containers and Conda definitions required to run pipeline with ARM. + + Use as follows: + nextflow run nf-core/rnaseq -profile ,arm + +---------------------------------------------------------------------------------------- +*/ + +process { + + // + // Tools that have native Conda builds for AMD and ARM + // + + withName: 'GTF_FILTER' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } + } + + withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } + } + + withName: 'DESEQ2_QC' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70a3d17733d2c21cff464c31a7a57438cea528bea84c675b7c474eaa7f075f57/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } + } + + withName: 'GTF2BED' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/896a3e55b2f664def0f8707420e1f53b4c447adb99fd6a1432a155c3403b9199/data' : 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } + } + + withName: 'MULTIQC_CUSTOM_BIOTYPE' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } + } + + withName: 'RSEM_MERGE_COUNTS' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } + } + + withName: 'UCSC_BEDCLIP' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f559cabdfda8b2937c4213d3a53547eb882b2fc8cc36ebfeff07481fa47823a/data' : 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } + } + + withName: 'UCSC_BEDGRAPHTOBIGWIG' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/389312a4a6022c5f5d2510dfa9bedb0491b36c8a27e8d842c05de00bc3b5be76/data' : 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } + } + + withName: 'CAT_FASTQ' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/38d3638640600b355110f9bca56c514e3cc068bf96b8b68f98cba2a59a053505/data' : 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } + } + + withName: 'RSEQC_TIN' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: 'RSEQC_READDISTRIBUTION' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: 'RSEQC_JUNCTIONSATURATION' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: 'RSEQC_READDUPLICATION' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: 'RSEQC_INFEREXPERIMENT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: 'RSEQC_BAMSTAT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: 'RSEQC_INNERDISTANCE' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: 'RSEQC_JUNCTIONANNOTATION' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: 'PICARD_MARKDUPLICATES' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0d4bbb10417a70d137a28da09329d9f9fbdf964a1cfeda24b05b618cae6b16f/data' : 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } + } + + withName: 'QUALIMAP_RNASEQ' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7aa0998788d327c6e7104c2c1e7bea2e8bb8fb7076ec5de3fdab4027e501b9a9/data' : 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } + } + + withName: 'SUBREAD_FEATURECOUNTS' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a81571bc8c4ac812adb76c51045a245041d7cc8923a2d7cc34a866588fead0c/data' : 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } + } + + withName: 'MULTIQC' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e97dcafc5915f90f863e70153f96bbe47963ebfd08383454d8bcd7263696e4e/data' : 'community.wave.seqera.io/library/multiqc:1.25.1--4062a515975cacba' } + } + + withName: 'STRINGTIE_STRINGTIE' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ebc6b1a27262420a5739330d369086b0d8c941a43b81d3fd0f741045bb3d46f/data' : 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } + } + + withName: 'UNTAR' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } + } + + withName: 'FQ_SUBSAMPLE' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } + } + + withName: 'DUPRADAR' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10141f8fd43964316d04214a5f7d99a62e11cdbab5bd2fcd4f7c3c06eca9f2f6/data' : 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } + } + + withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a7/a7d1ef576617b9790973bc9d178c4ef136a52b6337260c536cff6cd68f103b45/data' : 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } + } + + withName: 'STAR_GENOMEGENERATE' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } + } + + withName: 'STAR_ALIGN' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } + } + + withName: 'TXIMETA_TXIMPORT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f89ab1fef6e38e572ad1844d06f6d3d334d2b19a70c9e5d87bfc862b88728c23/data' : 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } + } + + withName: 'SORTMERNA' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } + } + + withName: 'PRESEQ_LCEXTRAP' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5ab535d5b4c88dc4837cab00919d4d5ea66dd4d6dc837d841886bef72145f435/data' : 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } + } + + withName: 'BEDTOOLS_GENOMECOV' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/519a920dacc643078823740486c40d30b9f555c493217d9f72db04901350e009/data' : 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } + } + + withName: 'BBMAP_BBSPLIT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63ca91c8bf7285296777de219e5d5a71d2a7de47599cbc94441aced7868a4f83/data' : 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } + } + + withName: 'FASTQC' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fd/fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017/data' : 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } + } + + withName: 'KALLISTO_QUANT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } + } + + withName: 'KALLISTO_INDEX' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } + } + + withName: 'SAMTOOLS_SORT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: 'SAMTOOLS_IDXSTATS' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: 'SAMTOOLS_INDEX' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: 'SAMTOOLS_FLAGSTAT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: 'SAMTOOLS_STATS' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: 'CUSTOM_CATADDITIONALFASTA' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c17acd739990ad12c06583f57b097014c2bde5a91d0977fd102864a82f95e136/data' : 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } + } + + withName: 'CUSTOM_TX2GENE' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/60/6029f43341dc0bea31d14c2ce4c779d7a48dfed6ecb29ce1630b8378c560c490/data' : 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } + } + + withName: 'CUSTOM_GETCHROMSIZES' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: 'UMITOOLS_PREPAREFORRSEM' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: 'UMITOOLS_EXTRACT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: 'UMITOOLS_DEDUP' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: 'GFFREAD' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e6db95013607b07689e38ee37a654d029236de77fdfde97fe1866f45d01e064/data' : 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } + } + + withName: 'FASTP' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7e/7ec6234f24305b9694b89de0352fff942ce1d68f840184020b0b9135bc54bda1/data' : 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } + } + + withName: 'SALMON_QUANT' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } + } + + withName: 'SALMON_INDEX' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } + } + + withName: 'GUNZIP' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } + } + + withName: 'TRIMGALORE' { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10e7b91ef06bdf5790120809afc8cf36aac0261b618d810c952d5afd60dd5ed2/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:2aa2fc797328573b' } + } + + // + // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in 'seqera' Conda channel. + // + + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } + } + + withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } + } + + withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } + } + + withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } + } + + // + // Tools currently unsupported for ARM + // + + //withName: 'HISAT2_ALIGN' { + // conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' + //} + + //withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + // conda = 'bioconda::hisat2=2.2.1' + //} + + // withName: 'KRAKEN2_KRAKEN2' { + // conda = 'bioconda::kraken2=2.1.3 coreutils=9.4 pigz=2.8' + //} + + // withName: 'BRACKEN_BRACKEN' { + // conda = 'bioconda::bracken=2.9' + //} +} diff --git a/docs/usage.md b/docs/usage.md index ad2aa4e26..851e20c7d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -116,6 +116,10 @@ If you would like to reduce the number of reads used in the analysis, for exampl ## Alignment options +:::note +The `--aligner hisat2` option is not currently supported using ARM architecture ('-profile arm') +::: + By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `--aligner star_salmon`) to map the raw FastQ reads to the reference genome, project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html). STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. Since the [RSEM](https://github.com/deweylab/RSEM) (i.e. `--aligner star_rsem`) workflow in the pipeline also uses STAR you should use the [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) aligner (i.e. `--aligner hisat2`) if you have memory limitations. You also have the option to pseudoalign and quantify your data directly with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) or [Kallisto](https://pachterlab.github.io/kallisto/) by specifying `salmon` or `kallisto` to the `--pseudo_aligner` parameter. The selected pseudoaligner will then be run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon or Kallisto in isolation. By default, the pipeline will use the genome fasta and gtf file to generate the transcripts fasta file, and then to build the Salmon index. You can override these parameters using the `--transcript_fasta` and `--salmon_index` parameters, respectively. @@ -298,6 +302,10 @@ By default, the input GTF file will be filtered to ensure that sequence names co ## Contamination screening options +:::note +The `--contaminant_screening` option is not currently available using ARM architecture ('-profile arm') +::: + The pipeline provides the option to scan unaligned reads for contamination from other species using [Kraken2](https://ccb.jhu.edu/software/kraken2/), with the possibility of applying corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). Since running Bracken is not computationally expensive, we recommend always using it to refine the abundance estimates generated by Kraken2. It is important to note that the accuracy of Kraken2 is [highly dependent on the database](https://doi.org/10.1099/mgen.0.000949) used. Specifically, it is [crucial](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is included in the database. If you are particularly concerned about certain contaminants, it may be beneficial to use a smaller, more focused database containing primarily those contaminants instead of the full standard database. Various pre-built databases [are available for download](https://benlangmead.github.io/aws-indexes/k2), and instructions for building a custom database can be found in the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Additionally, genomes of contaminants detected in previous sequencing experiments are available on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). @@ -356,6 +364,26 @@ genome: 'GRCh37' You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). +### Running on Linux ARM architectures + +:::warning +Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. +::: + +The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: + +```bash +nextflow run \ + nf-core/rnaseq \ + --input \ + --outdir \ + --gtf \ + --fasta \ + -profile docker,arm +``` + +This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operations. + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -420,6 +448,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. +- `arm` + - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. See [Running on Linux ARM architectures](#running-on-linux-arm-architectures). ### `-resume` diff --git a/modules.json b/modules.json index 6a263bfc8..9667d1b6b 100644 --- a/modules.json +++ b/modules.json @@ -7,48 +7,49 @@ "nf-core": { "bbmap/bbsplit": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "bedtools/genomecov": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963", "installed_by": ["modules"], "patch": "modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff" }, "bracken/bracken": { "branch": "master", - "git_sha": "c214fad97b328eb6d6233f779be9ba44814a9136", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"], + "patch": "modules/nf-core/cat/fastq/cat-fastq.diff" }, "custom/catadditionalfasta": { "branch": "master", - "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "custom/tx2gene": { "branch": "master", - "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "dupradar": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "fastqc": { @@ -58,48 +59,48 @@ }, "fq/subsample": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["fastq_subsample_fq_salmon", "modules"] }, "gffread": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "hisat2/align": { "branch": "master", - "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_align_hisat2"], "patch": "modules/nf-core/hisat2/align/hisat2-align.diff" }, "hisat2/build": { "branch": "master", - "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", - "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "kallisto/index": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "kallisto/quant": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "kraken2/kraken2": { "branch": "master", - "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { @@ -115,87 +116,87 @@ }, "preseq/lcextrap": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "qualimap/rnaseq": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "rsem/calculateexpression": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "rsem/preparereference": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "rseqc/bamstat": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/inferexperiment": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/innerdistance": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/junctionannotation": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/junctionsaturation": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/readdistribution": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/readduplication": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/tin": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "salmon/index": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["fastq_subsample_fq_salmon"] }, "salmon/quant": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": [ "bam_dedup_stats_samtools_umitools", "bam_markduplicates_picard", @@ -204,67 +205,70 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["bam_stats_samtools"] }, "sortmerna": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"], + "patch": "modules/nf-core/sortmerna/sortmerna.diff" }, "star/align": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab", + "installed_by": ["modules"], + "patch": "modules/nf-core/star/align/star-align.diff" }, "star/genomegenerate": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab", + "installed_by": ["modules"], + "patch": "modules/nf-core/star/genomegenerate/star-genomegenerate.diff" }, "stringtie/stringtie": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "summarizedexperiment/summarizedexperiment": { "branch": "master", - "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "trimgalore": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6", "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "tximeta/tximport": { "branch": "master", - "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "ucsc/bedclip": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "ucsc/bedgraphtobigwig": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "umitools/dedup": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_dedup_stats_samtools_umitools"] }, "umitools/extract": { @@ -274,12 +278,12 @@ }, "umitools/prepareforrsem": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } @@ -288,12 +292,12 @@ "nf-core": { "bam_dedup_stats_samtools_umitools": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["subworkflows"] }, "bam_markduplicates_picard": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["subworkflows"] }, "bam_rseqc": { @@ -303,12 +307,12 @@ }, "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["fastq_align_hisat2"] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": [ "bam_dedup_stats_samtools_umitools", "bam_markduplicates_picard", @@ -317,12 +321,12 @@ }, "bedgraph_bedclip_bedgraphtobigwig": { "branch": "master", - "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["subworkflows"] }, "fastq_align_hisat2": { "branch": "master", - "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["subworkflows"] }, "fastq_fastqc_umitools_fastp": { @@ -332,7 +336,7 @@ }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", - "git_sha": "4026bab16a91b1b0b18d80ff465819ca725f33fd", + "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { @@ -342,12 +346,12 @@ }, "fastq_subsample_fq_salmon": { "branch": "master", - "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "quantify_pseudo_alignment": { "branch": "master", - "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index dfd8936e1..a2f655067 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.01 + - bioconda::bbmap=39.10 diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index f308f6983..9eb53208c 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -5,8 +5,8 @@ process BBMAP_BBSPLIT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0': - 'biocontainers/bbmap:39.01--h5c4e2a8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': + 'biocontainers/bbmap:39.10--h92535d8_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml index f4e0a5ed5..c34196e47 100644 --- a/modules/nf-core/bbmap/bbsplit/meta.yml +++ b/modules/nf-core/bbmap/bbsplit/meta.yml @@ -8,64 +8,91 @@ keywords: - reference tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Directory to place generated index - pattern: "*" - - primary_ref: - type: file - description: Path to the primary reference - pattern: "*" - - other_ref_names: - type: list - description: List of other reference ids apart from the primary - - other_ref_paths: - type: list - description: Path to other references paths corresponding to "other_ref_names" - - only_build_index: - type: string - description: true = only build index; false = mapping + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Directory to place generated index + pattern: "*" + - - primary_ref: + type: file + description: Path to the primary reference + pattern: "*" + - - other_ref_names: + type: list + description: List of other reference ids apart from the primary + - other_ref_paths: + type: list + description: Path to other references paths corresponding to "other_ref_names" + - - only_build_index: + type: string + description: true = only build index; false = mapping output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Directory with index files - pattern: "bbsplit" + - bbsplit: + type: directory + description: Directory with index files + pattern: "bbsplit" - primary_fastq: - type: file - description: Output reads that map to the primary reference - pattern: "*primary*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*primary*fastq.gz": + type: file + description: Output reads that map to the primary reference + pattern: "*primary*fastq.gz" - all_fastq: - type: file - description: All reads mapping to any of the references - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: All reads mapping to any of the references + pattern: "*fastq.gz" - stats: - type: file - description: Tab-delimited text file containing mapping statistics - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*txt": + type: file + description: Tab-delimited text file containing mapping statistics + pattern: "*.txt" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap index 0d648d7d6..6bdc3c0d1 100644 --- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap @@ -9,26 +9,26 @@ "namelist.txt:md5,45e7a4cdc7a11a39ada56844ca3a1e30" ], [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T11:41:32.116928" + "timestamp": "2024-10-19T16:03:51.869574777" }, "sarscov2_se_fastq_fasta_chr22_fasta - index": { "content": [ [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T11:41:06.072212" + "timestamp": "2024-10-19T15:47:22.996403051" }, "sarscov2_se_fastq_fasta_chr22_fasta - index - stub": { "content": [ @@ -56,7 +56,7 @@ ] ], "5": [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ], "all_fastq": [ @@ -81,15 +81,15 @@ ], "versions": [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T11:45:21.48352" + "timestamp": "2024-10-19T16:03:10.27746726" }, "sarscov2_se_fastq_fasta_chr22_fasta - stub": { "content": [ @@ -139,7 +139,7 @@ ] ], "5": [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ], "all_fastq": [ [ @@ -186,14 +186,14 @@ ] ], "versions": [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T11:51:38.805111" + "timestamp": "2024-10-19T16:04:18.416324262" } } \ No newline at end of file diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff index 53d7e34df..17aa9eb2d 100644 --- a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -2,14 +2,14 @@ Changes in module 'nf-core/bedtools/genomecov' Changes in 'bedtools/genomecov/main.nf': --- modules/nf-core/bedtools/genomecov/main.nf +++ modules/nf-core/bedtools/genomecov/main.nf -@@ -4,8 +4,8 @@ +@@ -3,9 +3,7 @@ + label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': -+ 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" ++ container 'nf-core/bedtools_coreutils:a623c13f66d5262b' input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 91869ec23..10a99d439 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,9 +3,7 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" + container 'nf-core/bedtools_coreutils:a623c13f66d5262b' input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml index 2b2385e3e..41b1f8f49 100644 --- a/modules/nf-core/bedtools/genomecov/meta.yml +++ b/modules/nf-core/bedtools/genomecov/meta.yml @@ -1,5 +1,6 @@ name: bedtools_genomecov -description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. +description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) + summaries of feature coverage (e.g., aligned sequences) for a given genome. keywords: - bed - bam @@ -12,39 +13,50 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - scale: - type: integer - description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch - - sizes: - type: file - description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column - - extension: - type: string - description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - scale: + type: integer + description: Number containing the scale factor for the output. Set to 1 to + disable. Setting to a value other than 1 will also get the -bg bedgraph output + format as this is required for this command switch + - - sizes: + type: file + description: Tab-delimited table of chromosome names in the first column and + chromosome sizes in the second column + - - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", + ".tab", etc.) It is set arbitrarily by the user and corresponds to the file + format which depends on arguments. + - - sort: + type: boolean + description: Sort the output output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - genomecov: - type: file - description: Computed genome coverage file - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Computed genome coverage file + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bracken/bracken/environment.yml b/modules/nf-core/bracken/bracken/environment.yml index 6eb5b1b9a..b96b00d7a 100644 --- a/modules/nf-core/bracken/bracken/environment.yml +++ b/modules/nf-core/bracken/bracken/environment.yml @@ -1,7 +1,5 @@ -name: bracken_bracken channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bracken=2.9" diff --git a/modules/nf-core/bracken/bracken/meta.yml b/modules/nf-core/bracken/bracken/meta.yml index b7ff4489f..85a267efc 100644 --- a/modules/nf-core/bracken/bracken/meta.yml +++ b/modules/nf-core/bracken/bracken/meta.yml @@ -7,44 +7,61 @@ keywords: - kraken2 tools: - bracken: - description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample. homepage: https://ccb.jhu.edu/software/bracken/ documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual tool_dev_url: https://github.com/jenniferlu717/Bracken doi: "10.7717/peerj-cs.104" licence: ["GPL v3"] + identifier: biotools:bracken input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kraken_report: - type: file - description: TSV file with six columns coming from kraken2 output - pattern: "*.{tsv}" - - database: - type: file - description: Directory containing the kraken2/Bracken files for analysis - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kraken_report: + type: file + description: TSV file with six columns coming from kraken2 output + pattern: "*.{tsv}" + - - database: + type: file + description: Directory containing the kraken2/Bracken files for analysis + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reports: - type: file - description: TSV output report of the re-estimated abundances - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{tsv}" + - bracken_report: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{tsv}" - txt: - type: file - description: TXT file of bracken corrected results of Kraken2 report output - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.txt" + - bracken_kraken_style_report: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test b/modules/nf-core/bracken/bracken/tests/main.nf.test index 9d2105ded..3085f3f89 100644 --- a/modules/nf-core/bracken/bracken/tests/main.nf.test +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test @@ -4,12 +4,6 @@ nextflow_process { script "../main.nf" process "BRACKEN_BRACKEN" - tag "modules" - tag "modules_nfcore" - tag "bracken" - tag "bracken/bracken" - tag "kraken2/kraken2" - tag "untar" setup { run ("UNTAR") { diff --git a/modules/nf-core/cat/fastq/cat-fastq.diff b/modules/nf-core/cat/fastq/cat-fastq.diff new file mode 100644 index 000000000..0d3832c04 --- /dev/null +++ b/modules/nf-core/cat/fastq/cat-fastq.diff @@ -0,0 +1,37 @@ +Changes in module 'nf-core/cat/fastq' +'modules/nf-core/cat/fastq/nextflow.config' was created +Changes in 'cat/fastq/main.nf': +--- modules/nf-core/cat/fastq/main.nf ++++ modules/nf-core/cat/fastq/main.nf +@@ -3,9 +3,7 @@ + label 'process_single' + + conda "${moduleDir}/environment.yml" +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : +- 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" ++ container 'nf-core/coreutils:9.5--ae99c88a9b28c264' + + input: + tuple val(meta), path(reads, stageAs: "input*/*") + +'modules/nf-core/cat/fastq/meta.yml' is unchanged +'modules/nf-core/cat/fastq/environment.yml' is unchanged +'modules/nf-core/cat/fastq/tests/main.nf.test.snap' is unchanged +Changes in 'cat/fastq/tests/main.nf.test': +--- modules/nf-core/cat/fastq/tests/main.nf.test ++++ modules/nf-core/cat/fastq/tests/main.nf.test +@@ -5,10 +5,6 @@ + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" +- tag "modules" +- tag "modules_nfcore" +- tag "cat" +- tag "cat/fastq" + + test("test_cat_fastq_single_end") { + + +'modules/nf-core/cat/fastq/tests/tags.yml' was removed +************************************************************ diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index c7eb9bd1c..71e04c3d7 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::coreutils=8.30 + - conda-forge::coreutils=9.5 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index b68e5f911..6f4f96e34 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,9 +3,7 @@ process CAT_FASTQ { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + container 'nf-core/coreutils:9.5--ae99c88a9b28c264' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index db4ac3c79..91ff2fb5f 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -10,30 +10,33 @@ tools: The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files to be concatenated. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Merged fastq file - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index aec119a94..f8689a1ce 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:30:39.816981" + "timestamp": "2024-10-19T20:02:07.519211144" }, "test_cat_fastq_single_end_same_name": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:32:35.229332" + "timestamp": "2024-10-19T20:02:31.618628921" }, "test_cat_fastq_single_end_single_file": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:34:00.058829" + "timestamp": "2024-10-19T20:02:57.904149581" }, "test_cat_fastq_paired_end_same_name": { "content": [ @@ -120,7 +120,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -135,15 +135,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:33:33.031555" + "timestamp": "2024-10-19T20:02:44.577183829" }, "test_cat_fastq_single_end - stub": { "content": [ @@ -158,7 +158,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -170,15 +170,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:28.244999" + "timestamp": "2024-10-19T20:03:10.603734777" }, "test_cat_fastq_paired_end_same_name - stub": { "content": [ @@ -196,7 +196,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -211,15 +211,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:57.070911" + "timestamp": "2024-10-19T20:03:46.041808828" }, "test_cat_fastq_single_end_same_name - stub": { "content": [ @@ -234,7 +234,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -246,15 +246,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:46.796254" + "timestamp": "2024-10-19T20:03:34.13865402" }, "test_cat_fastq_paired_end": { "content": [ @@ -272,7 +272,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -287,15 +287,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:32:02.270935" + "timestamp": "2024-10-19T20:02:19.64383573" }, "test_cat_fastq_paired_end - stub": { "content": [ @@ -313,7 +313,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -328,15 +328,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:37.807553" + "timestamp": "2024-10-19T20:03:22.597246066" }, "test_cat_fastq_single_end_single_file - stub": { "content": [ @@ -351,7 +351,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -363,14 +363,14 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:14:51.861264" + "timestamp": "2024-10-19T20:03:58.44849001" } } \ No newline at end of file diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index 1d80d11a9..2000006c4 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::python=3.9.5 + - conda-forge::python=3.12.2 diff --git a/modules/nf-core/custom/catadditionalfasta/main.nf b/modules/nf-core/custom/catadditionalfasta/main.nf index 88ce4954b..9925ca322 100644 --- a/modules/nf-core/custom/catadditionalfasta/main.nf +++ b/modules/nf-core/custom/catadditionalfasta/main.nf @@ -3,8 +3,8 @@ process CUSTOM_CATADDITIONALFASTA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'biocontainers/python:3.9--1' }" + 'https://depot.galaxyproject.org/singularity/python:3.12' : + 'biocontainers/python:3.12' }" input: tuple val(meta), path(fasta), path(gtf) diff --git a/modules/nf-core/custom/catadditionalfasta/meta.yml b/modules/nf-core/custom/catadditionalfasta/meta.yml index 8a9505d30..e6c313d39 100644 --- a/modules/nf-core/custom/catadditionalfasta/meta.yml +++ b/modules/nf-core/custom/catadditionalfasta/meta.yml @@ -1,60 +1,67 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_catadditionalfasta" -description: Custom module to Add a new fasta file to an old one and update an associated GTF +description: Custom module to Add a new fasta file to an old one and update an associated + GTF keywords: - fasta - gtf - genomics tools: - "custom": - description: "Custom module to Add a new fasta file to an old one and update an associated GTF" + description: "Custom module to Add a new fasta file to an old one and update an + associated GTF" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/catadditionalfasta/main.nf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing fasta information - - meta2: - type: map - description: | - Groovy Map containing additional fasta information - - fasta: - type: file - description: FASTA-format sequence file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: GTF-format annotation file for fasta - pattern: "*.gtf" - - add_fasta: - type: file - description: FASTA-format file of additional sequences - pattern: "*.fa" - - biotype: - type: string - description: Biotype to apply to new GTF entries - + - - meta: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: FASTA-format sequence file + pattern: "*.{fasta,fa}" + - gtf: + type: file + description: GTF-format annotation file for fasta + pattern: "*.gtf" + - - meta2: + type: map + description: | + Groovy Map containing additional fasta information + - add_fasta: + type: file + description: FASTA-format file of additional sequences + pattern: "*.fa" + - - biotype: + type: string + description: Biotype to apply to new GTF entries output: - - meta: - type: map - description: | - Groovy Map containing fasta information - fasta: - type: file - description: FASTA-format combined sequence file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing fasta information + - "*/*.fasta": + type: file + description: FASTA-format combined sequence file + pattern: "*.{fasta,fa}" - gtf: - type: file - description: GTF-format combined annotation file - pattern: "*.gtf" + - meta: + type: map + description: | + Groovy Map containing fasta information + - "*/*.gtf": + type: file + description: GTF-format combined annotation file + pattern: "*.gtf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py index 06b4c253a..c7351e568 100755 --- a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py +++ b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py @@ -114,16 +114,8 @@ def main() -> None: fasta_to_gtf("$add_fasta", f"{add_name}.gtf", "$biotype") # Concatenate new fasta to existing fasta, and the GTF we just generated to the GTF - genome_name = ( - "$params.genome" - if "$params.genome" != "null" - else os.path.splitext(os.path.basename("$fasta"))[0] - ) - output_prefix = ( - "$task.ext.prefix" - if "$task.ext.prefix" != "null" - else f"{genome_name}_{add_name}" - ) + genome_name = "$params.genome" if "$params.genome" != "null" else os.path.splitext(os.path.basename("$fasta"))[0] + output_prefix = "$task.ext.prefix" if "$task.ext.prefix" != "null" else f"{genome_name}_{add_name}" os.mkdir("out") os.system(f"cat $fasta $add_fasta > out/{output_prefix}.fasta") diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap index 4767fd9a0..6dd1afeb1 100644 --- a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap +++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,26f47339777a265af57338ac7f0f8798" + "versions.yml:md5,5917ae30ad1ee71ad6b62659d5b628d1" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:19:28.965471" + "timestamp": "2024-10-19T21:07:02.01253345" }, "sarscov2 - fastq - gtf - stub": { "content": [ @@ -77,9 +77,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:19:38.549677" + "timestamp": "2024-10-19T21:07:12.9817063" } } \ No newline at end of file diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index da2df5e43..2bcd47ee1 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 3edf7c221..d8c7405c6 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -4,8 +4,8 @@ process CUSTOM_GETCHROMSIZES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml index 529be07e4..2a0e8da0a 100644 --- a/modules/nf-core/custom/getchromsizes/meta.yml +++ b/modules/nf-core/custom/getchromsizes/meta.yml @@ -12,38 +12,53 @@ tools: tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta,fna,fas}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta,fna,fas}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sizes: - type: file - description: File containing chromosome lengths - pattern: "*.{sizes}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sizes": + type: file + description: File containing chromosome lengths + pattern: "*.{sizes}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap index c37b284d7..d2072e22c 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap @@ -27,7 +27,7 @@ ] ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -54,15 +54,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:38:36.927106" + "timestamp": "2024-10-18T10:11:37.459094476" }, "test_custom_getchromsizes": { "content": [ @@ -87,7 +87,7 @@ ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -109,15 +109,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T13:22:34.14237" + "timestamp": "2024-10-18T10:11:01.526301351" }, "test_custom_getchromsizes_bgzip": { "content": [ @@ -147,7 +147,7 @@ ] ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -174,15 +174,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T13:23:06.241379" + "timestamp": "2024-10-18T10:11:14.32456385" }, "test_custom_getchromsizes - stub": { "content": [ @@ -207,7 +207,7 @@ ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -229,14 +229,14 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:24:05.697845" + "timestamp": "2024-10-18T10:11:26.505487624" } } \ No newline at end of file diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index 9f5f9fb9b..9824d0c27 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - python=3.9.5 + - python=3.10.4 diff --git a/modules/nf-core/custom/tx2gene/main.nf b/modules/nf-core/custom/tx2gene/main.nf index 99c00aa06..eed5e97b1 100644 --- a/modules/nf-core/custom/tx2gene/main.nf +++ b/modules/nf-core/custom/tx2gene/main.nf @@ -4,8 +4,8 @@ process CUSTOM_TX2GENE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'biocontainers/python:3.9--1' }" + 'https://depot.galaxyproject.org/singularity/python:3.10.4' : + 'biocontainers/python:3.10.4' }" input: tuple val(meta), path(gtf) diff --git a/modules/nf-core/custom/tx2gene/meta.yml b/modules/nf-core/custom/tx2gene/meta.yml index d991bf1be..8254afa08 100644 --- a/modules/nf-core/custom/tx2gene/meta.yml +++ b/modules/nf-core/custom/tx2gene/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_tx2gene" -description: Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. +description: Make a transcript/gene mapping from a GTF and cross-reference with transcript + quantifications. keywords: - gene - gtf @@ -14,51 +14,51 @@ tools: check it against transcript quantifications" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information related to the GTF file - e.g. `[ id:'yeast' ]` - - gtf: - type: file - description: An annotation file of the reference genome in GTF format - pattern: "*.gtf" - - meta2: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - quants: - type: directory - description: Paths to subdirectories corresponding to - sample-wise runs of Salmon or Kallisto - - quant_type: - type: string - description: Quantification type, 'kallisto' or 'salmon' - - id: - type: string - description: Gene ID attribute in the GTF file (default= gene_id) - - extra: - type: string - description: Extra gene attribute in the GTF file (default= gene_name) - + - - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - gtf: + type: file + description: An annotation file of the reference genome in GTF format + pattern: "*.gtf" + - - meta2: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - '"quants/*"': + type: file + description: quants file + - - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' + - - id: + type: string + description: Gene ID attribute in the GTF file (default= gene_id) + - - extra: + type: string + description: Extra gene attribute in the GTF file (default= gene_name) output: - - meta: - type: map - description: | - Groovy Map containing reference information related to the GTF file - e.g. `[ id:'yeast' ]` - tx2gene: - type: file - description: A transcript/ gene mapping table in TSV format - pattern: "*.tx2gene.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - "*tx2gene.tsv": + type: file + description: A transcript/ gene mapping table in TSV format + pattern: "*.tx2gene.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap index c19f10f71..2be5fe547 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840" ], "tx2gene": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:13:11.305047" + "timestamp": "2024-10-18T10:24:12.19104487" }, "saccharomyces_cerevisiae - gtf - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + "versions.yml:md5,48194bffef8cb833e82e31166f3d486c" ], "tx2gene": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + "versions.yml:md5,48194bffef8cb833e82e31166f3d486c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T15:15:34.064489" + "timestamp": "2024-10-18T10:24:24.729694098" } } \ No newline at end of file diff --git a/modules/nf-core/dupradar/meta.yml b/modules/nf-core/dupradar/meta.yml index 95960ae98..a532519fe 100644 --- a/modules/nf-core/dupradar/meta.yml +++ b/modules/nf-core/dupradar/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "dupradar" description: Assessment of duplication rates in RNA-Seq datasets @@ -14,71 +13,109 @@ tools: tool_dev_url: "https://github.com/ssayols/dupRadar" doi: "10.1186/s12859-016-1276-2" licence: ["GPL v3"] + identifier: biotools:dupradar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file containing read alignments - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'human' ] - - gtf: - type: file - description: Genomic features annotation in GTF or SAF - pattern: "*.{gtf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/SAM file containing read alignments + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'human' ] + - gtf: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - scatter2d: - type: file - description: PDF duplication rate against total read count plot - pattern: "*_duprateExpDens.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_duprateExpDens.pdf": + type: file + description: PDF duplication rate against total read count plot + pattern: "*_duprateExpDens.pdf" - boxplot: - type: file - description: | - PDF duplication rate ~ total reads per kilobase (RPK) boxplot - pattern: "*_duprateExpBoxplot.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_duprateExpBoxplot.pdf": + type: file + description: | + PDF duplication rate ~ total reads per kilobase (RPK) boxplot + pattern: "*_duprateExpBoxplot.pdf" - hist: - type: file - description: | - PDF expression histogram - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_expressionHist.pdf": + type: file + description: | + PDF expression histogram + pattern: "*.pdf" - dupmatrix: - type: file - description: | - Text file containing tags falling on the features described in the GTF - file - pattern: "*_dupMatrix.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_dupMatrix.txt": + type: file + description: | + Text file containing tags falling on the features described in the GTF + file + pattern: "*_dupMatrix.txt" - intercept_slope: - type: file - description: | - Text file containing intercept and slope from dupRadar modelling - pattern: "*_intercept_slope.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_intercept_slope.txt": + type: file + description: | + Text file containing intercept and slope from dupRadar modelling + pattern: "*_intercept_slope.txt" - multiqc: - type: file - description: | - dupRadar files for passing to MultiQC - pattern: "*_multiqc.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_mqc.txt": + type: file + description: | + dupRadar files for passing to MultiQC + pattern: "*_multiqc.txt" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 8dfecc184..159404d08 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -11,66 +11,100 @@ tools: documentation: https://github.com/OpenGene/fastp doi: 10.1093/bioinformatics/bty560 licence: ["MIT"] + identifier: biotools:fastp input: - - meta: - type: map - description: | - Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. If you wish to run interleaved paired-end data, supply as single-end data - but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - adapter_fasta: - type: file - description: File in FASTA format containing possible adapters to remove. - pattern: "*.{fasta,fna,fas,fa}" - - discard_trimmed_pass: - type: boolean - description: Specify true to not write any reads that pass trimming thresholds. | - This can be used to use fastp for the output report only. - - save_trimmed_fail: - type: boolean - description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz` - - save_merged: - type: boolean - description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` + - - meta: + type: map + description: | + Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. If you wish to run interleaved paired-end data, supply as single-end data + but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. + - - adapter_fasta: + type: file + description: File in FASTA format containing possible adapters to remove. + pattern: "*.{fasta,fna,fas,fa}" + - - discard_trimmed_pass: + type: boolean + description: Specify true to not write any reads that pass trimming thresholds. + | This can be used to use fastp for the output report only. + - - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds + ending in `*.fail.fastq.gz` + - - save_merged: + type: boolean + description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified/unmerged fastq reads - pattern: "*fastp.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastp.fastq.gz": + type: file + description: The trimmed/modified/unmerged fastq reads + pattern: "*fastp.fastq.gz" - json: - type: file - description: Results in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Results in JSON format + pattern: "*.json" - html: - type: file - description: Results in HTML format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Results in HTML format + pattern: "*.html" - log: - type: file - description: fastq log file - pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: fastq log file + pattern: "*.log" - reads_fail: - type: file - description: Reads the failed the preprocessing - pattern: "*fail.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fail.fastq.gz": + type: file + description: Reads the failed the preprocessing + pattern: "*fail.fastq.gz" - reads_merged: - type: file - description: Reads that were successfully merged - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Reads that were successfully merged + pattern: "*.{merged.fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index eaba9339b..74b146083 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fq=0.9.1 + - bioconda::fq=0.12.0 diff --git a/modules/nf-core/fq/subsample/main.nf b/modules/nf-core/fq/subsample/main.nf index a8e647bb1..d66f0cd1a 100644 --- a/modules/nf-core/fq/subsample/main.nf +++ b/modules/nf-core/fq/subsample/main.nf @@ -4,8 +4,8 @@ process FQ_SUBSAMPLE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0': - 'biocontainers/fq:0.9.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/fq:0.12.0--h9ee0642_0': + 'biocontainers/fq:0.12.0--h9ee0642_0' }" input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/fq/subsample/meta.yml b/modules/nf-core/fq/subsample/meta.yml index 6c5e87f3e..7d91b0d9a 100644 --- a/modules/nf-core/fq/subsample/meta.yml +++ b/modules/nf-core/fq/subsample/meta.yml @@ -1,5 +1,6 @@ name: "fq_subsample" -description: fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args. +description: fq subsample outputs a subset of records from single or paired FASTQ + files. This requires a seed (--seed) to be set in ext.args. keywords: - fastq - fq @@ -11,30 +12,33 @@ tools: documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FASTQ file - pattern: "*.{fq,fastq}{,.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FASTQ file + pattern: "*.{fq,fastq}{,.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Randomly sampled FASTQ files. - pattern: "*_R[12].fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Randomly sampled FASTQ files. + pattern: "*_R[12].fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/fq/subsample/tests/main.nf.test.snap b/modules/nf-core/fq/subsample/tests/main.nf.test.snap index 739c626d7..cf0b0f254 100644 --- a/modules/nf-core/fq/subsample/tests/main.nf.test.snap +++ b/modules/nf-core/fq/subsample/tests/main.nf.test.snap @@ -15,7 +15,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -30,15 +30,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T08:26:12.163153" + "timestamp": "2024-10-19T16:33:49.881713827" }, "test_fq_subsample_probability": { "content": [ @@ -56,7 +56,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -71,15 +71,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:57:15.446336" + "timestamp": "2024-10-19T16:33:38.284916869" }, "test_fq_subsample_single - stub": { "content": [ @@ -97,7 +97,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -112,56 +112,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T08:26:55.736374" - }, - "test_fq_subsample_no_args - sub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ], - "fastq": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T08:25:42.190405" + "timestamp": "2024-10-19T16:34:47.477222088" }, "test_fq_subsample_record_count": { "content": [ @@ -179,7 +138,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -194,56 +153,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:57:23.920058" - }, - "stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ], - "fastq": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-20T17:16:10.090213" + "timestamp": "2024-10-19T16:34:02.461958921" }, "test_fq_subsample_single": { "content": [ @@ -258,7 +176,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -270,15 +188,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:57:31.908993" + "timestamp": "2024-10-19T16:34:27.295010129" }, "test_fq_subsample_no_args": { "content": [ @@ -298,10 +216,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-10-17T11:17:09.761156" + "timestamp": "2024-10-19T16:33:26.427718685" }, "test_fq_subsample_no_input": { "content": [ @@ -321,10 +239,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-10-17T11:17:37.555824" + "timestamp": "2024-10-19T16:35:00.624040224" }, "test_fq_subsample_record_count - stub": { "content": [ @@ -342,48 +260,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ], - "fastq": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T08:26:33.873553" - }, - "test_fq_subsample_no_input - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -398,14 +275,14 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T08:27:21.793136" + "timestamp": "2024-10-19T16:34:14.613246906" } } \ No newline at end of file diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index c06028208..bebe7f575 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -1,53 +1,73 @@ name: gffread -description: Validate, filter, convert and perform various other operations on GFF files +description: Validate, filter, convert and perform various other operations on GFF + files keywords: - gff - conversion - validation tools: - gffread: - description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more. + description: GFF/GTF utility providing format conversions, region filtering, FASTA + sequence extraction and more. homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread tool_dev_url: https://github.com/gpertea/gffread doi: 10.12688/f1000research.23297.1 licence: ["MIT"] + identifier: biotools:gffread input: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - - gff: - type: file - description: A reference file in either the GFF3, GFF2 or GTF format. - pattern: "*.{gff, gtf}" - - fasta: - type: file - description: A multi-fasta file with the genomic sequences - pattern: "*.{fasta,fa,faa,fas,fsa}" + - - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - gff: + type: file + description: A reference file in either the GFF3, GFF2 or GTF format. + pattern: "*.{gff, gtf}" + - - fasta: + type: file + description: A multi-fasta file with the genomic sequences + pattern: "*.{fasta,fa,faa,fas,fsa}" output: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - gtf: - type: file - description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present - pattern: "*.{gtf}" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gtf": + type: file + description: GTF file resulting from the conversion of the GFF input file if + '-T' argument is present + pattern: "*.{gtf}" - gffread_gff: - type: file - description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gff3": + type: file + description: GFF3 file resulting from the conversion of the GFF input file if + '-T' argument is absent + pattern: "*.gff3" - gffread_fasta: - type: file - description: Fasta file produced when either of '-w', '-x', '-y' parameters is present - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.fasta": + type: file + description: Fasta file produced when either of '-w', '-x', '-y' parameters + is present + pattern: "*.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index f32973a0a..9066c0353 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,25 +10,32 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml index b23eab75b..d869c5d56 100644 --- a/modules/nf-core/hisat2/align/meta.yml +++ b/modules/nf-core/hisat2/align/meta.yml @@ -7,58 +7,79 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - index: - type: file - description: HISAT2 genome index file - pattern: "*.ht2" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - index: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - summary: - type: file - description: Aligment log - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Aligment log + pattern: "*.log" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: Output FastQ file + pattern: "*fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" - "@ramprasadn" diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml index 6c28eb21c..3272f8e05 100644 --- a/modules/nf-core/hisat2/build/meta.yml +++ b/modules/nf-core/hisat2/build/meta.yml @@ -8,53 +8,58 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fa,fasta,fna}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gtf: - type: file - description: Reference gtf annotation file - pattern: "*.{gtf}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fa,fasta,fna}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - index: - type: file - description: HISAT2 genome index file - pattern: "*.ht2" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - hisat2: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/hisat2/extractsplicesites/meta.yml b/modules/nf-core/hisat2/extractsplicesites/meta.yml index 40d77ce00..c1bdc9e65 100644 --- a/modules/nf-core/hisat2/extractsplicesites/meta.yml +++ b/modules/nf-core/hisat2/extractsplicesites/meta.yml @@ -7,35 +7,40 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gtf: - type: file - description: Reference gtf annotation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] + - txt: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - "*.splice_sites.txt": + type: file + description: Splice sites in txt file + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{splice_sites.txt}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" - "@ramprasadn" diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 27be64918..773f42484 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto=0.51.1 diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index bbd226c93..73a5f7a95 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -4,8 +4,8 @@ process KALLISTO_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kallisto:0.48.0--h15996b6_2': - 'biocontainers/kallisto:0.48.0--h15996b6_2' }" + 'https://depot.galaxyproject.org/singularity/kallisto:0.51.1--heb0cbe2_0': + 'biocontainers/kallisto:0.51.1--heb0cbe2_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/kallisto/index/meta.yml b/modules/nf-core/kallisto/index/meta.yml index d366aeb45..4541074ed 100644 --- a/modules/nf-core/kallisto/index/meta.yml +++ b/modules/nf-core/kallisto/index/meta.yml @@ -6,35 +6,40 @@ keywords: - index tools: - kallisto: - description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. + description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq + data, or more generally of target sequences using high-throughput sequencing + reads. homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto licence: ["BSD-2-Clause"] + identifier: biotools:kallisto input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: genome fasta file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: genome fasta file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - index: - type: directory - description: Kallisto genome index - pattern: "*.idx" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - kallisto: + type: directory + description: Kallisto genome index + pattern: "*.idx" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ggabernet" maintainers: diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test b/modules/nf-core/kallisto/index/tests/main.nf.test index c5e86e87c..bdb824012 100644 --- a/modules/nf-core/kallisto/index/tests/main.nf.test +++ b/modules/nf-core/kallisto/index/tests/main.nf.test @@ -20,7 +20,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert path(process.out.index.get(0).get(1)).exists() }, + { assert snapshot(process.out.versions).match() } ) } } diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test.snap b/modules/nf-core/kallisto/index/tests/main.nf.test.snap index b2891a4a3..42ba6c310 100644 --- a/modules/nf-core/kallisto/index/tests/main.nf.test.snap +++ b/modules/nf-core/kallisto/index/tests/main.nf.test.snap @@ -13,7 +13,7 @@ ] ], "1": [ - "versions.yml:md5,178f9b57d4228edc356911d571b958a4" + "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" ], "index": [ [ @@ -26,47 +26,26 @@ ] ], "versions": [ - "versions.yml:md5,178f9b57d4228edc356911d571b958a4" + "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:27:54.464205" + "timestamp": "2024-10-19T18:51:55.402665844" }, "sarscov2 transcriptome.fasta": { "content": [ - { - "0": [ - [ - { - "id": "transcriptome" - }, - "kallisto:md5,ba657b396f8449f5c85b0563cdaa8346" - ] - ], - "1": [ - "versions.yml:md5,178f9b57d4228edc356911d571b958a4" - ], - "index": [ - [ - { - "id": "transcriptome" - }, - "kallisto:md5,ba657b396f8449f5c85b0563cdaa8346" - ] - ], - "versions": [ - "versions.yml:md5,178f9b57d4228edc356911d571b958a4" - ] - } + [ + "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-19T09:17:56.733532" + "timestamp": "2024-10-19T18:51:42.328144373" } } \ No newline at end of file diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index 27be64918..773f42484 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto=0.51.1 diff --git a/modules/nf-core/kallisto/quant/main.nf b/modules/nf-core/kallisto/quant/main.nf index acfc8c9c7..edd0fb203 100644 --- a/modules/nf-core/kallisto/quant/main.nf +++ b/modules/nf-core/kallisto/quant/main.nf @@ -4,8 +4,8 @@ process KALLISTO_QUANT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kallisto:0.48.0--h15996b6_2': - 'biocontainers/kallisto:0.48.0--h15996b6_2' }" + 'https://depot.galaxyproject.org/singularity/kallisto:0.51.1--heb0cbe2_0': + 'biocontainers/kallisto:0.51.1--heb0cbe2_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kallisto/quant/meta.yml b/modules/nf-core/kallisto/quant/meta.yml index d5100290f..329268a17 100644 --- a/modules/nf-core/kallisto/quant/meta.yml +++ b/modules/nf-core/kallisto/quant/meta.yml @@ -6,71 +6,85 @@ keywords: - pseudoalignment tools: - "kallisto": - description: "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads." + description: "Quantifying abundances of transcripts from RNA-Seq data, or more + generally of target sequences using high-throughput sequencing reads." homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto doi: "10.1038/nbt.3519" licence: ["BSD_2_clause"] + identifier: biotools:kallisto input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fastq,fastq.gz}" - - index: - type: file - description: Kallisto genome index. - pattern: "*.idx" - - gtf: - type: file - description: Optional gtf file for translation of transcripts into genomic coordinates. - pattern: "*.gtf" - - chromosomes: - type: file - description: Optional tab separated file with chromosome names and lengths. - pattern: "*.tsv" - - fragment_length: - type: integer - description: For single-end mode only, the estimated average fragment length. - - fragment_length_sd: - type: integer - description: For single-end mode only, the estimated standard deviation of the fragment length. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fastq,fastq.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: Kallisto genome index. + pattern: "*.idx" + - - gtf: + type: file + description: Optional gtf file for translation of transcripts into genomic coordinates. + pattern: "*.gtf" + - - chromosomes: + type: file + description: Optional tab separated file with chromosome names and lengths. + pattern: "*.tsv" + - - fragment_length: + type: integer + description: For single-end mode only, the estimated average fragment length. + - - fragment_length_sd: + type: integer + description: For single-end mode only, the estimated standard deviation of the + fragment length. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Kallisto output file + - json_info: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.run_info.json": + type: file + description: JSON file containing information about the run + pattern: "*.run_info.json" - log: - type: file - description: File containing log information from running kallisto quant - pattern: "*.log.txt" - - abundance: - type: file - description: Plaintext file of the abundance estimates - pattern: "abundance.tsv" - - abundance_hdf5: - type: file - description: | - A HDF5 binary file containing run info, abundance estimates, bootstrap - estimates, and transcript length information - pattern: "abundance.h5" - - run_info: - type: file - description: A json file containing information about the run - pattern: "run_info.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File containing log information from running kallisto quant + pattern: "*.log.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/kallisto/quant/tests/main.nf.test.snap b/modules/nf-core/kallisto/quant/tests/main.nf.test.snap index cf0d73304..db1aa10e6 100644 --- a/modules/nf-core/kallisto/quant/tests/main.nf.test.snap +++ b/modules/nf-core/kallisto/quant/tests/main.nf.test.snap @@ -8,18 +8,18 @@ "id": "test", "single_end": false }, - "test.log:md5,8a5987f8e779cd12ca708e2212f771f5" + "test.log:md5,cb46ef02463f63fec5aac31a4adcac94" ] ], [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:25:27.043048" + "timestamp": "2024-10-19T16:46:09.603634413" }, "sarscov2 paired-end - stub": { "content": [ @@ -54,7 +54,7 @@ ] ], "3": [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ], "json_info": [ [ @@ -86,15 +86,15 @@ ] ], "versions": [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:26:04.484652" + "timestamp": "2024-10-19T16:46:38.620702213" }, "sarscov2 single-end - stub": { "content": [ @@ -129,7 +129,7 @@ ] ], "3": [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ], "json_info": [ [ @@ -161,15 +161,15 @@ ] ], "versions": [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:25:46.479136" + "timestamp": "2024-10-19T16:46:24.255840154" }, "sarscov2 single-end": { "content": [ @@ -180,17 +180,17 @@ "id": "test", "single_end": true }, - "test.log:md5,9c166f0c50cd4fdbdbf1bff9d5d8aba2" + "test.log:md5,0cad96e4108b2ea1c152ad063198b21f" ] ], [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:25:08.348876" + "timestamp": "2024-10-19T16:45:56.782215718" } } \ No newline at end of file diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml index 0c067feeb..ba776d315 100644 --- a/modules/nf-core/kraken2/kraken2/environment.yml +++ b/modules/nf-core/kraken2/kraken2/environment.yml @@ -1,8 +1,6 @@ -name: kraken2_kraken2 channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::kraken2=2.1.3" - "coreutils=9.4" diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml index 7909ffe7e..869376467 100644 --- a/modules/nf-core/kraken2/kraken2/meta.yml +++ b/modules/nf-core/kraken2/kraken2/meta.yml @@ -13,63 +13,84 @@ tools: documentation: https://github.com/DerrickWood/kraken2/wiki/Manual doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] + identifier: biotools:kraken2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - db: - type: directory - description: Kraken2 database - - save_output_fastqs: - type: string - description: | - If true, optional commands are added to save classified and unclassified reads - as fastq files - - save_reads_assignment: - type: string - description: | - If true, an optional command is added to save a file reporting the taxonomic - classification of each input read + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - db: + type: directory + description: Kraken2 database + - - save_output_fastqs: + type: string + description: | + If true, optional commands are added to save classified and unclassified reads + as fastq files + - - save_reads_assignment: + type: string + description: | + If true, an optional command is added to save a file reporting the taxonomic + classification of each input read output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - classified_reads_fastq: - type: file - description: | - Reads classified as belonging to any of the taxa - on the Kraken2 database. - pattern: "*{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.classified{.,_}*": + type: file + description: | + Reads classified as belonging to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" - unclassified_reads_fastq: - type: file - description: | - Reads not classified to any of the taxa - on the Kraken2 database. - pattern: "*{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unclassified{.,_}*": + type: file + description: | + Reads not classified to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" - classified_reads_assignment: - type: file - description: | - Kraken2 output file indicating the taxonomic assignment of - each input read + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classifiedreads.txt": + type: file + description: | + Kraken2 output file indicating the taxonomic assignment of + each input read - report: - type: file - description: | - Kraken2 report containing stats about classified - and not classifed reads. - pattern: "*.{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: | + Kraken2 report containing stats about classified + and not classifed reads. + pattern: "*.{report.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test index c0843df29..60adc5ef0 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -2,11 +2,6 @@ nextflow_process { name "Test Process KRAKEN2_KRAKEN2" script "../main.nf" process "KRAKEN2_KRAKEN2" - tag "modules" - tag "modules_nfcore" - tag "untar" - tag "kraken2" - tag "kraken2/kraken2" setup { run("UNTAR") { diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 926d7aece..6300d3f33 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::preseq=3.1.2 + - bioconda::preseq=3.2.0 diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 3fec468e9..540a5fb27 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -5,8 +5,8 @@ process PRESEQ_LCEXTRAP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - 'biocontainers/preseq:3.1.2--h445547b_2' }" + 'https://depot.galaxyproject.org/singularity/preseq:3.2.0--hdcf5f25_6': + 'biocontainers/preseq:3.2.0--hdcf5f25_6' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/meta.yml b/modules/nf-core/preseq/lcextrap/meta.yml index c00fa8eef..28fb449ca 100644 --- a/modules/nf-core/preseq/lcextrap/meta.yml +++ b/modules/nf-core/preseq/lcextrap/meta.yml @@ -1,44 +1,55 @@ name: preseq_lcextrap -description: Software for predicting library complexity and genome coverage in high-throughput sequencing +description: Software for predicting library complexity and genome coverage in high-throughput + sequencing keywords: - preseq - library - complexity tools: - preseq: - description: Software for predicting library complexity and genome coverage in high-throughput sequencing + description: Software for predicting library complexity and genome coverage in + high-throughput sequencing homepage: http://smithlabresearch.org/software/preseq/ documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf tool_dev_url: https://github.com/smithlabcode/preseq licence: ["GPL"] + identifier: biotools:preseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - lc_extrap: - type: file - description: File containing output of Preseq lcextrap - pattern: "*.{lc_extrap.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lc_extrap.txt": + type: file + description: File containing output of Preseq lcextrap + pattern: "*.{lc_extrap.txt}" - log: - type: file - description: Log file containing stderr produced by Preseq - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stderr produced by Preseq + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap index 3f95cd498..c725d8e89 100644 --- a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap +++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap @@ -30,14 +30,14 @@ "single_end - versions": { "content": [ [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T17:20:40.74601" + "timestamp": "2024-10-19T16:55:55.821665692" }, "sarscov2 - single_end - stub": { "content": [ @@ -61,7 +61,7 @@ ] ], "2": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ], "lc_extrap": [ [ @@ -82,27 +82,27 @@ ] ], "versions": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T18:43:12.689062" + "timestamp": "2024-10-19T16:56:11.779385911" }, "paired_end - versions": { "content": [ [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T17:20:52.02843" + "timestamp": "2024-10-19T16:56:31.353046182" }, "single_end - log": { "content": [ @@ -154,7 +154,7 @@ ] ], "2": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ], "lc_extrap": [ [ @@ -175,14 +175,14 @@ ] ], "versions": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T18:43:32.569811" + "timestamp": "2024-10-19T16:56:45.034808313" } } \ No newline at end of file diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml index 6f766e4f5..a730261b5 100644 --- a/modules/nf-core/qualimap/rnaseq/meta.yml +++ b/modules/nf-core/qualimap/rnaseq/meta.yml @@ -15,39 +15,42 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/rsem/calculateexpression/meta.yml b/modules/nf-core/rsem/calculateexpression/meta.yml index e6d580e9b..0a7fbe1b3 100644 --- a/modules/nf-core/rsem/calculateexpression/meta.yml +++ b/modules/nf-core/rsem/calculateexpression/meta.yml @@ -12,53 +12,97 @@ tools: documentation: https://github.com/deweylab/RSEM doi: 10.1186/1471-2105-12-323 licence: ["GPL-3.0-or-later"] + identifier: biotools:rsem input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input reads for quantification - pattern: "*.fastq.gz" - - index: - type: file - description: RSEM index - pattern: "rsem/*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input reads for quantification + pattern: "*.fastq.gz" + - - index: + type: file + description: RSEM index + pattern: "rsem/*" output: - counts_gene: - type: file - description: Expression counts on gene level - pattern: "*.genes.results" - - counts_transctips: - type: file - description: Expression counts on transcript level - pattern: "*.isoforms.results" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.genes.results": + type: file + description: Expression counts on gene level + pattern: "*.genes.results" + - counts_transcript: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.isoforms.results": + type: file + description: Expression counts on transcript level + pattern: "*.isoforms.results" - stat: - type: file - description: RSEM statistics - pattern: "*.stat" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.stat": + type: file + description: RSEM statistics + pattern: "*.stat" - logs: - type: file - description: RSEM logs - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: RSEM logs + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - bam_star: - type: file - description: BAM file generated by STAR (optional) - pattern: "*.STAR.genome.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.STAR.genome.bam": + type: file + description: BAM file generated by STAR (optional) + pattern: "*.STAR.genome.bam" - bam_genome: - type: file - description: Genome BAM file (optional) - pattern: "*.genome.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.genome.bam: + type: file + description: Genome BAM file (optional) + pattern: "*.genome.bam" - bam_transcript: - type: file - description: Transcript BAM file (optional) - pattern: "*.transcript.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.transcript.bam: + type: file + description: Transcript BAM file (optional) + pattern: "*.transcript.bam" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rsem/preparereference/meta.yml b/modules/nf-core/rsem/preparereference/meta.yml index 05aa44fe6..e95f4a2ae 100644 --- a/modules/nf-core/rsem/preparereference/meta.yml +++ b/modules/nf-core/rsem/preparereference/meta.yml @@ -12,28 +12,32 @@ tools: documentation: https://github.com/deweylab/RSEM doi: 10.1186/1471-2105-12-323 licence: ["GPL-3.0-or-later"] + identifier: biotools:rsem input: - - fasta: - type: file - description: The Fasta file of the reference genome - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: The GTF file of the reference genome - pattern: "*.gtf" + - - fasta: + type: file + description: The Fasta file of the reference genome + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: The GTF file of the reference genome + pattern: "*.gtf" output: - - rsem: - type: directory - description: RSEM index directory - pattern: "rsem" + - index: + - rsem: + type: directory + description: RSEM index directory + pattern: "rsem" - transcript_fasta: - type: file - description: Fasta file of transcripts - pattern: "rsem/*transcripts.fa" + - "*transcripts.fa": + type: file + description: Fasta file of transcripts + pattern: "rsem/*transcripts.fa" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/bamstat/meta.yml b/modules/nf-core/rseqc/bamstat/meta.yml index 72745310c..d69f05442 100644 --- a/modules/nf-core/rseqc/bamstat/meta.yml +++ b/modules/nf-core/rseqc/bamstat/meta.yml @@ -13,25 +13,32 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the bam file to calculate statistics of - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the bam file to calculate statistics of + pattern: "*.{bam}" output: - txt: - type: file - description: bam statistics report - pattern: "*.bam_stat.txt" + - meta: + type: file + description: bam statistics report + pattern: "*.bam_stat.txt" + - "*.bam_stat.txt": + type: file + description: bam statistics report + pattern: "*.bam_stat.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/bamstat/tests/main.nf.test b/modules/nf-core/rseqc/bamstat/tests/main.nf.test index fd6fc0811..7af50092d 100644 --- a/modules/nf-core/rseqc/bamstat/tests/main.nf.test +++ b/modules/nf-core/rseqc/bamstat/tests/main.nf.test @@ -3,6 +3,8 @@ nextflow_process { name "Test Process RSEQC_BAMSTAT" script "../main.nf" process "RSEQC_BAMSTAT" + + config "./nextflow.config" test("sarscov2 - [meta] - bam") { diff --git a/modules/nf-core/rseqc/inferexperiment/meta.yml b/modules/nf-core/rseqc/inferexperiment/meta.yml index d9b9ff63e..3ac757289 100644 --- a/modules/nf-core/rseqc/inferexperiment/meta.yml +++ b/modules/nf-core/rseqc/inferexperiment/meta.yml @@ -13,29 +13,36 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the bam file to calculate statistics of - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the bam file to calculate statistics of + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: infer_experiment results report - pattern: "*.infer_experiment.txt" + - meta: + type: file + description: infer_experiment results report + pattern: "*.infer_experiment.txt" + - "*.infer_experiment.txt": + type: file + description: infer_experiment results report + pattern: "*.infer_experiment.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/innerdistance/meta.yml b/modules/nf-core/rseqc/innerdistance/meta.yml index d0a5bf181..358e4d160 100644 --- a/modules/nf-core/rseqc/innerdistance/meta.yml +++ b/modules/nf-core/rseqc/innerdistance/meta.yml @@ -13,45 +13,72 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - distance: - type: file - description: the inner distances - pattern: "*.inner_distance.txt" + - meta: + type: file + description: the inner distances + pattern: "*.inner_distance.txt" + - "*distance.txt": + type: file + description: the inner distances + pattern: "*.inner_distance.txt" - freq: - type: file - description: frequencies of different insert sizes - pattern: "*.inner_distance_freq.txt" + - meta: + type: file + description: frequencies of different insert sizes + pattern: "*.inner_distance_freq.txt" + - "*freq.txt": + type: file + description: frequencies of different insert sizes + pattern: "*.inner_distance_freq.txt" - mean: - type: file - description: mean/median values of inner distances - pattern: "*.inner_distance_mean.txt" + - meta: + type: file + description: mean/median values of inner distances + pattern: "*.inner_distance_mean.txt" + - "*mean.txt": + type: file + description: mean/median values of inner distances + pattern: "*.inner_distance_mean.txt" - pdf: - type: file - description: distribution plot of inner distances - pattern: "*.inner_distance_plot.pdf" + - meta: + type: file + description: distribution plot of inner distances + pattern: "*.inner_distance_plot.pdf" + - "*.pdf": + type: file + description: distribution plot of inner distances + pattern: "*.inner_distance_plot.pdf" - rscript: - type: file - description: script to reproduce the plot - pattern: "*.inner_distance_plot.R" + - meta: + type: file + description: script to reproduce the plot + pattern: "*.inner_distance_plot.R" + - "*.r": + type: file + description: script to reproduce the plot + pattern: "*.inner_distance_plot.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/junctionannotation/meta.yml b/modules/nf-core/rseqc/junctionannotation/meta.yml index a88aa2db3..0622ee43b 100644 --- a/modules/nf-core/rseqc/junctionannotation/meta.yml +++ b/modules/nf-core/rseqc/junctionannotation/meta.yml @@ -13,53 +13,90 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: + - xls: + - meta: + type: file + description: xls file with junction information + pattern: "*.xls" + - "*.xls": + type: file + description: xls file with junction information + pattern: "*.xls" + - rscript: + - meta: + type: file + description: Rscript to reproduce the plots + pattern: "*.r" + - "*.r": + type: file + description: Rscript to reproduce the plots + pattern: "*.r" + - log: + - meta: + type: file + description: Log file of execution + pattern: "*.junction_annotation.log" + - "*.log": + type: file + description: Log file of execution + pattern: "*.junction_annotation.log" - bed: - type: file - description: bed file of annotated junctions - pattern: "*.junction.bed" + - meta: + type: file + description: bed file of annotated junctions + pattern: "*.junction.bed" + - "*.junction.bed": + type: file + description: bed file of annotated junctions + pattern: "*.junction.bed" - interact_bed: - type: file - description: Interact bed file - pattern: "*.Interact.bed" - - xls: - type: file - description: xls file with junction information - pattern: "*.xls" + - meta: + type: file + description: Interact bed file + pattern: "*.Interact.bed" + - "*.Interact.bed": + type: file + description: Interact bed file + pattern: "*.Interact.bed" - pdf: - type: file - description: junction plot - pattern: "*.junction.pdf" + - meta: + type: file + description: junction plot + pattern: "*.junction.pdf" + - "*junction.pdf": + type: file + description: junction plot + pattern: "*.junction.pdf" - events_pdf: - type: file - description: events plot - pattern: "*.events.pdf" - - rscript: - type: file - description: Rscript to reproduce the plots - pattern: "*.r" - - log: - type: file - description: Log file of execution - pattern: "*.junction_annotation.log" + - meta: + type: file + description: events plot + pattern: "*.events.pdf" + - "*events.pdf": + type: file + description: events plot + pattern: "*.events.pdf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/junctionsaturation/meta.yml b/modules/nf-core/rseqc/junctionsaturation/meta.yml index 19ae3f52d..b6f422dc7 100644 --- a/modules/nf-core/rseqc/junctionsaturation/meta.yml +++ b/modules/nf-core/rseqc/junctionsaturation/meta.yml @@ -13,33 +13,45 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - pdf: - type: file - description: Junction saturation report - pattern: "*.pdf" + - meta: + type: file + description: Junction saturation report + pattern: "*.pdf" + - "*.pdf": + type: file + description: Junction saturation report + pattern: "*.pdf" - rscript: - type: file - description: Junction saturation R-script - pattern: "*.r" + - meta: + type: file + description: Junction saturation R-script + pattern: "*.r" + - "*.r": + type: file + description: Junction saturation R-script + pattern: "*.r" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/readdistribution/meta.yml b/modules/nf-core/rseqc/readdistribution/meta.yml index 989792faa..578200abb 100644 --- a/modules/nf-core/rseqc/readdistribution/meta.yml +++ b/modules/nf-core/rseqc/readdistribution/meta.yml @@ -13,29 +13,36 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: the read distribution report - pattern: "*.read_distribution.txt" + - meta: + type: file + description: the read distribution report + pattern: "*.read_distribution.txt" + - "*.read_distribution.txt": + type: file + description: the read distribution report + pattern: "*.read_distribution.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/readduplication/meta.yml b/modules/nf-core/rseqc/readduplication/meta.yml index 4b24d3032..ef94122e9 100644 --- a/modules/nf-core/rseqc/readduplication/meta.yml +++ b/modules/nf-core/rseqc/readduplication/meta.yml @@ -14,41 +14,59 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" output: - seq_xls: - type: file - description: Read duplication rate determined from mapping position of read - pattern: "*seq.DupRate.xls" + - meta: + type: file + description: Read duplication rate determined from mapping position of read + pattern: "*seq.DupRate.xls" + - "*seq.DupRate.xls": + type: file + description: Read duplication rate determined from mapping position of read + pattern: "*seq.DupRate.xls" - pos_xls: - type: file - description: Read duplication rate determined from sequence of read - pattern: "*pos.DupRate.xls" + - meta: + type: file + description: Read duplication rate determined from sequence of read + pattern: "*pos.DupRate.xls" + - "*pos.DupRate.xls": + type: file + description: Read duplication rate determined from sequence of read + pattern: "*pos.DupRate.xls" - pdf: - type: file - description: plot of duplication rate - pattern: "*.pdf" + - meta: + type: file + description: plot of duplication rate + pattern: "*.pdf" + - "*.pdf": + type: file + description: plot of duplication rate + pattern: "*.pdf" - rscript: - type: file - description: script to reproduce the plot - pattern: "*.R" + - meta: + type: file + description: script to reproduce the plot + pattern: "*.R" + - "*.r": + type: file + description: script to reproduce the plot + pattern: "*.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/tin/meta.yml b/modules/nf-core/rseqc/tin/meta.yml index f760bb2f4..6e363ecd8 100644 --- a/modules/nf-core/rseqc/tin/meta.yml +++ b/modules/nf-core/rseqc/tin/meta.yml @@ -13,37 +13,49 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - bai: - type: file - description: Index for input BAM file - pattern: "*.{bai}" - - bed: - type: file - description: BED file containing the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - bai: + type: file + description: Index for input BAM file + pattern: "*.{bai}" + - - bed: + type: file + description: BED file containing the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: TXT file containing tin.py results summary - pattern: "*.txt" + - meta: + type: file + description: TXT file containing tin.py results summary + pattern: "*.txt" + - "*.txt": + type: file + description: TXT file containing tin.py results summary + pattern: "*.txt" - xls: - type: file - description: XLS file containing tin.py results - pattern: "*.xls" + - meta: + type: file + description: XLS file containing tin.py results + pattern: "*.xls" + - "*.xls": + type: file + description: XLS file containing tin.py results + pattern: "*.xls" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index 471164faa..b3f75777e 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon=1.10.3 diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index e755d9a34..3d653c0d0 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -4,8 +4,8 @@ process SALMON_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' : - 'biocontainers/salmon:1.10.1--h7e5ed60_0' }" + 'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' : + 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: path genome_fasta diff --git a/modules/nf-core/salmon/index/meta.yml b/modules/nf-core/salmon/index/meta.yml index fd94dd274..48486a2bb 100644 --- a/modules/nf-core/salmon/index/meta.yml +++ b/modules/nf-core/salmon/index/meta.yml @@ -13,22 +13,25 @@ tools: manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ["GPL-3.0-or-later"] + identifier: biotools:salmon input: - - genome_fasta: - type: file - description: Fasta file of the reference genome - - transcriptome_fasta: - type: file - description: Fasta file of the reference transcriptome + - - genome_fasta: + type: file + description: Fasta file of the reference genome + - - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome output: - index: - type: directory - description: Folder containing the star index files - pattern: "salmon" + - salmon: + type: directory + description: Folder containing the star index files + pattern: "salmon" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salmon/index/tests/main.nf.test.snap b/modules/nf-core/salmon/index/tests/main.nf.test.snap index 703e455c5..e5899b511 100644 --- a/modules/nf-core/salmon/index/tests/main.nf.test.snap +++ b/modules/nf-core/salmon/index/tests/main.nf.test.snap @@ -2,25 +2,25 @@ "versions": { "content": [ [ - "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42" + "versions.yml:md5,85337fa0a286ea35073ee5260974e307" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-22T14:26:33.32036" + "timestamp": "2024-10-18T10:00:47.087293189" }, "versions stub": { "content": [ [ - "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42" + "versions.yml:md5,85337fa0a286ea35073ee5260974e307" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-23T09:47:58.828124" + "timestamp": "2024-10-18T10:01:03.89824494" } } \ No newline at end of file diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 471164faa..b3f75777e 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon=1.10.3 diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 6c528b240..f1e3b5cda 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -4,8 +4,8 @@ process SALMON_QUANT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' : - 'biocontainers/salmon:1.10.1--h7e5ed60_0' }" + 'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' : + 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/salmon/quant/meta.yml b/modules/nf-core/salmon/quant/meta.yml index a2faf589a..4cacde0f0 100644 --- a/modules/nf-core/salmon/quant/meta.yml +++ b/modules/nf-core/salmon/quant/meta.yml @@ -13,47 +13,69 @@ tools: manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ["GPL-3.0-or-later"] + identifier: biotools:salmon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files for single-end or paired-end data. - Multiple single-end fastqs or pairs of paired-end fastqs are - handled. - - index: - type: directory - description: Folder containing the star index files - - gtf: - type: file - description: GTF of the reference transcriptome - - transcript_fasta: - type: file - description: Fasta file of the reference transcriptome - - alignment_mode: - type: boolean - description: whether to run salmon in alignment mode - - lib_type: - type: string - description: | - Override library type inferred based on strandedness defined in meta object + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files for single-end or paired-end data. + Multiple single-end fastqs or pairs of paired-end fastqs are + handled. + - - index: + type: directory + description: Folder containing the star index files + - - gtf: + type: file + description: GTF of the reference transcriptome + - - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome + - - alignment_mode: + type: boolean + description: whether to run salmon in alignment mode + - - lib_type: + type: string + description: | + Override library type inferred based on strandedness defined in meta object output: - results: - type: directory - description: Folder containing the quantification results for a specific sample - pattern: "${prefix}" + - meta: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" + - ${prefix}: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" - json_info: - type: file - description: File containing meta information from Salmon quant - pattern: "*info.json" + - meta: + type: file + description: File containing meta information from Salmon quant + pattern: "*info.json" + - "*info.json": + type: file + description: File containing meta information from Salmon quant + pattern: "*info.json" + - lib_format_counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*lib_format_counts.json": + type: file + description: File containing the library format counts + pattern: "*lib_format_counts.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test.snap b/modules/nf-core/salmon/quant/tests/main.nf.test.snap index 547ce2de1..ea22a80ce 100644 --- a/modules/nf-core/salmon/quant/tests/main.nf.test.snap +++ b/modules/nf-core/salmon/quant/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2 - single_end": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -15,15 +15,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:22.424672" + "timestamp": "2024-10-18T10:01:16.989080539" }, "sarscov2 - single_end stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -36,15 +36,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:32.292277" + "timestamp": "2024-10-18T10:01:29.340996235" }, "sarscov2 - single_end lib type A": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -57,15 +57,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:42.656382" + "timestamp": "2024-10-18T10:01:43.056167576" }, "sarscov2 - pair_end multiple": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -78,15 +78,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:33.03647" + "timestamp": "2024-10-18T10:03:05.500792631" }, "sarscov2 - pair_end multiple stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -99,15 +99,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:43.388379" + "timestamp": "2024-10-18T10:03:26.428959203" }, "sarscov2 - single_end lib type A stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -120,15 +120,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:52.612664" + "timestamp": "2024-10-18T10:02:03.420850208" }, "sarscov2 - pair_end": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -141,15 +141,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:05.577881" + "timestamp": "2024-10-18T10:02:16.130074696" }, "sarscov2 - pair_end stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -162,9 +162,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:15.286461" + "timestamp": "2024-10-18T10:02:39.470004547" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 754d84b73..4a4997274 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 97991358e..cdc4c2544 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -1,5 +1,6 @@ name: samtools_flagstat -description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type +description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG + type keywords: - stats - mapping @@ -17,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.flagstat": + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 23989c612..04c3852b2 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ], "flagstat": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:28.002887" + "timestamp": "2024-09-16T08:02:58.866491759" }, "BAM": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ], "flagstat": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:13.330971" + "timestamp": "2024-09-16T08:02:47.383332837" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 2ea2a5ccd..c4b5a0a3f 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index 344e92a3f..f0a6bcb2a 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -18,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.idxstats": + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index a5ac8104e..2cc89a3b8 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ], "idxstats": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:56.180093" + "timestamp": "2024-09-16T08:11:56.466856235" }, "bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ], "idxstats": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:41.408704" + "timestamp": "2024-09-16T08:11:46.311550359" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e002585b9..311756102 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 01a4ee03e..db8df0d50 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -15,38 +15,52 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - csi: - type: file - description: CSI index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI index file + pattern: "*.{csi}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 799d199ce..72d65e81a 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:53.9057" + "timestamp": "2024-09-16T08:21:25.261127166" }, "crai - stub": { "content": [ @@ -65,7 +65,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -83,15 +83,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:45.931558" + "timestamp": "2024-09-16T08:21:12.653194876" }, "bai - stub": { "content": [ @@ -112,7 +112,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -130,28 +130,28 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:34.807525" + "timestamp": "2024-09-16T08:21:01.854932651" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:52:55.688799" + "timestamp": "2024-09-16T08:20:51.485364222" }, "crai": { "content": [ @@ -172,7 +172,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -190,15 +190,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:17.609533" + "timestamp": "2024-09-16T08:20:40.518873972" }, "bai": { "content": [ @@ -219,7 +219,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -237,14 +237,14 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:04.16585" + "timestamp": "2024-09-16T08:20:21.184050361" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 8e019099c..caf3c61a8 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,19 +4,19 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta) , path(bam) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 341a7d0eb..a9dbec5a8 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -15,52 +15,73 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file(s) - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta,fna}" - optional: true + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file(s) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Sorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM file + pattern: "*.{cram}" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 41c2fca7f..14d9d73d8 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -35,6 +35,40 @@ nextflow_process { } } + test("multiple bam") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + test("cram") { config "./nextflow_cram.config" @@ -94,6 +128,36 @@ nextflow_process { } } + test("multiple bam - stub") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("cram - stub") { options "-stub" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index da38d5d15..469891fe3 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:19:37.196205" + "timestamp": "2024-09-16T08:49:58.207549273" }, "bam - stub": { "content": [ @@ -57,7 +57,7 @@ ] ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ [ @@ -84,15 +84,15 @@ ] ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:54:46.580756" + "timestamp": "2024-09-16T08:50:08.630951018" }, "cram - stub": { "content": [ @@ -122,7 +122,7 @@ ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ @@ -149,15 +149,110 @@ ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:57:30.505698" + "timestamp": "2024-09-16T08:50:19.061912443" + }, + "multiple bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:59:55.479443" + }, + "multiple bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "4": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "versions": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:36:13.781404" }, "bam": { "content": [ @@ -167,7 +262,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" ] ], [ @@ -180,13 +275,13 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.09.0" }, - "timestamp": "2024-07-22T15:54:25.872954" + "timestamp": "2024-10-08T11:59:46.372244" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 982bc28e7..493525a9e 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 735ff8122..77b020f76 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -16,43 +16,46 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing samtools stats output + pattern: "*.{stats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@FriederikeHanssen" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 3828f3788..df507be7a 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,c9d39b38c22de2057fc2f89949090975" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -20,19 +20,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,c9d39b38c22de2057fc2f89949090975" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:20:24.885816" + "timestamp": "2024-09-16T09:29:16.767396182" }, "bam - stub": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:20:39.310713" + "timestamp": "2024-09-16T09:29:29.721580274" }, "cram - stub": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:21:04.771199" + "timestamp": "2024-09-16T09:29:53.567964304" }, "bam": { "content": [ @@ -113,11 +113,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -125,18 +125,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:19:06.645466" + "timestamp": "2024-09-16T09:28:50.73610604" } } \ No newline at end of file diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index fab44081f..75d586704 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sortmerna=4.3.6 + - seqera::sortmerna=4.3.7 diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 7c17e500c..2ea221c59 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -3,9 +3,7 @@ process SORTMERNA { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' : - 'biocontainers/sortmerna:4.3.6--h9ee0642_0' }" + container 'nf-core/sortmerna:4.3.7--6502243397c065ba' input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sortmerna/meta.yml b/modules/nf-core/sortmerna/meta.yml index c0a2a581f..3b43d006d 100644 --- a/modules/nf-core/sortmerna/meta.yml +++ b/modules/nf-core/sortmerna/meta.yml @@ -8,67 +8,84 @@ keywords: - ribosomal RNA tools: - SortMeRNA: - description: The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. + description: The core algorithm is based on approximate seeds and allows for sensitive + analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from + metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, + fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart + aligned and rejected reads into two files. Additional applications include clustering + and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with + Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. homepage: https://hpc.nih.gov/apps/sortmeRNA.html documentation: https://github.com/biocore/sortmerna/wiki/ licence: ["GPL-3.0-or-later"] + identifier: biotools:sortmerna input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fastas: - type: file - description: | - Path to reference file(s) - - meta3: - type: map - description: | - Groovy Map containing index information - e.g. [ id:'test' ] - - index: - type: directory - description: | - Path to index directory of a previous sortmerna run + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fastas: + type: file + description: | + Path to reference file(s) + - - meta3: + type: map + description: | + Groovy Map containing index information + e.g. [ id:'test' ] + - index: + type: directory + description: | + Path to index directory of a previous sortmerna run output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ], or reference information from an - indexing-only run - reads: - type: file - description: The filtered fastq reads - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ], or reference information from an + indexing-only run + - "*non_rRNA.fastq.gz": + type: file + description: The filtered fastq reads + pattern: "*fastq.gz" - log: - type: file - description: SortMeRNA log file - pattern: "*sortmerna.log" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ], or reference information from an + indexing-only run + - "*.log": + type: file + description: SortMeRNA log file + pattern: "*sortmerna.log" - index: - type: directory - description: | - Path to index directory generated by sortmern + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - idx: + type: directory + description: | + Path to index directory generated by sortmern - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@mashehu" diff --git a/modules/nf-core/sortmerna/sortmerna.diff b/modules/nf-core/sortmerna/sortmerna.diff new file mode 100644 index 000000000..5e37cabf8 --- /dev/null +++ b/modules/nf-core/sortmerna/sortmerna.diff @@ -0,0 +1,579 @@ +Changes in module 'nf-core/sortmerna' +'modules/nf-core/sortmerna/nextflow.config' was created +Changes in 'sortmerna/main.nf': +--- modules/nf-core/sortmerna/main.nf ++++ modules/nf-core/sortmerna/main.nf +@@ -3,9 +3,7 @@ + label 'process_high' + + conda "${moduleDir}/environment.yml" +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' : +- 'biocontainers/sortmerna:4.3.6--h9ee0642_0' }" ++ container 'nf-core/sortmerna:4.3.7--6502243397c065ba' + + input: + tuple val(meta), path(reads) + +'modules/nf-core/sortmerna/meta.yml' is unchanged +Changes in 'sortmerna/environment.yml': +--- modules/nf-core/sortmerna/environment.yml ++++ modules/nf-core/sortmerna/environment.yml +@@ -2,4 +2,4 @@ + - conda-forge + - bioconda + dependencies: +- - bioconda::sortmerna=4.3.6 ++ - seqera::sortmerna=4.3.7 + +Changes in 'sortmerna/tests/main.nf.test.snap': +--- modules/nf-core/sortmerna/tests/main.nf.test.snap ++++ modules/nf-core/sortmerna/tests/main.nf.test.snap +@@ -2,14 +2,14 @@ + "versions_paired_end_stub": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:27:11.223149" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:01.533875274" + }, + "index_paired_end_stub": { + "content": [ +@@ -25,48 +25,22 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:24:25.384097178" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:01.450465678" + }, + "versions_paired_end": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:27:04.517155" +- }, +- "versions_single_end_stub": { +- "content": [ +- [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-01T12:10:35.228450189" +- }, +- "sarscov2 single_end_match": { +- "content": [ +- [ +- "test.non_rRNA.fastq.gz", +- "test.sortmerna.log", +- "{id=test}" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:28:23.20327" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:48.811712136" + }, + "index_only_stub": { + "content": [ +@@ -82,44 +56,79 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:00:47.128504164" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:38:56.554562414" ++ }, ++ "sarscov2 single_end_match": { ++ "content": [ ++ [ ++ "test.non_rRNA.fastq.gz", ++ "test.sortmerna.log", ++ "{id=test}" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:09.015863183" ++ }, ++ "versions_single_end_stub": { ++ "content": [ ++ [ ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:28.573618474" + }, + "index_single_end_premade_index": { + "content": [ + [ +- [ +- { +- "id": "test2" +- }, +- [ +- "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", +- "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", +- "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", +- "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" +- ] +- ] +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:01:53.832643452" ++ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T12:02:37.578808801" + }, + "versions_single_end_premade_index": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:01:53.902154982" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:14.269803641" ++ }, ++ "sarscov2 indexing only": { ++ "content": [ ++ [ ++ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ++ ], ++ [ ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T11:59:11.705138075" + }, + "sarscov2 paired_end-for_stub_match": { + "content": [ +@@ -133,32 +142,24 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:28:56.063579" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:01.365507281" + }, + "index_paired_end": { + "content": [ + [ +- [ +- { +- "id": "test2" +- }, +- [ +- "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", +- "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", +- "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", +- "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" +- ] +- ] +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:24:14.272659781" ++ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T12:01:29.664107565" + }, + "sarscov2 single_end_premade_index_match_stub": { + "content": [ +@@ -169,10 +170,10 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:05:01.913287272" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:28.87594616" + }, + "sarscov2 single_end-for_stub_match": { + "content": [ +@@ -183,10 +184,10 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:28:29.197913" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:28.458349619" + }, + "sarscov2 paired_end_match": { + "content": [ +@@ -200,46 +201,46 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:28:49.914992" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:48.667990373" + }, + "versions_single_end": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:36:27.14244294" +- }, +- "versions_index_only": { +- "content": [ +- [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:00:35.609161481" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:09.110655329" + }, + "versions_single_end_premade_index_stub": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:05:02.059858431" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:29.097777821" ++ }, ++ "versions_index_only_stub": { ++ "content": [ ++ [ ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:38:56.592840673" + }, + "index_single_end_stub": { + "content": [ +@@ -255,22 +256,10 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:23:58.068772508" +- }, +- "versions_index_only_stub": { +- "content": [ +- [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:00:47.169402699" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:28.516407836" + }, + "index_single_end_premade_index_stub": { + "content": [ +@@ -286,54 +275,24 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:05:01.953316205" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:28.988436085" + }, + "index_single_end": { + "content": [ + [ +- [ +- { +- "id": "test2" +- }, +- [ +- "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", +- "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", +- "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", +- "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" +- ] +- ] +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:36:26.88061978" +- }, +- "index_index_only": { +- "content": [ +- [ +- [ +- { +- "id": "test2" +- }, +- [ +- "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", +- "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", +- "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", +- "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" +- ] +- ] +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:00:35.34089252" ++ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T12:00:30.580004574" + }, + "sarscov2 single_end_premade_index_match": { + "content": [ +@@ -344,9 +303,9 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:01:53.797737296" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:14.075100849" + } + } +Changes in 'sortmerna/tests/main.nf.test': +--- modules/nf-core/sortmerna/tests/main.nf.test ++++ modules/nf-core/sortmerna/tests/main.nf.test +@@ -24,11 +24,17 @@ + } + + then { ++ def index_files = file(process.out.index[0][1]).listFiles() ++ .findAll { !it.name.endsWith('.stats') } ++ .sort { a, b -> a.name <=> b.name } ++ + assertAll( + { assert process.success }, + { assert ! process.out.reads }, +- { assert snapshot(process.out.index).match("index_index_only") }, +- { assert snapshot(process.out.versions).match("versions_index_only") } ++ { assert snapshot( ++ index_files, ++ process.out.versions ++ ).match() }, + ) + } + +@@ -79,6 +85,10 @@ + } + + then { ++ def index_files = file(process.out.index[0][1]).listFiles() ++ .findAll { !it.name.endsWith('.stats') } ++ .sort { a, b -> a.name <=> b.name } ++ + assertAll( + { assert process.success }, + { assert process.out.reads }, +@@ -92,7 +102,7 @@ + ).sort() + ).match("sarscov2 single_end_match") + }, +- { assert snapshot(process.out.index).match("index_single_end") }, ++ { assert snapshot(index_files).match("index_single_end") }, + { assert snapshot(process.out.versions).match("versions_single_end") } + ) + } +@@ -157,6 +167,10 @@ + } + + then { ++ def index_files = file(process.out.index[0][1]).listFiles() ++ .findAll { !it.name.endsWith('.stats') } ++ .sort { a, b -> a.name <=> b.name } ++ + assertAll( + { assert process.success }, + { assert process.out.reads }, +@@ -170,7 +184,7 @@ + ).sort() + ).match("sarscov2 paired_end_match") + }, +- { assert snapshot(process.out.index).match("index_paired_end") }, ++ { assert snapshot(index_files).match("index_paired_end") }, + { assert snapshot(process.out.versions).match("versions_paired_end") } + ) + } +@@ -252,6 +266,10 @@ + } + + then { ++ def index_files = file(process.out.index[0][1]).listFiles() ++ .findAll { !it.name.endsWith('.stats') } ++ .sort { a, b -> a.name <=> b.name } ++ + assertAll( + { assert process.success }, + { assert process.out.reads }, +@@ -265,7 +283,7 @@ + ).sort() + ).match("sarscov2 single_end_premade_index_match") + }, +- { assert snapshot(process.out.index).match("index_single_end_premade_index") }, ++ { assert snapshot(index_files).match("index_single_end_premade_index") }, + { assert snapshot(process.out.versions).match("versions_single_end_premade_index") } + ) + } + +'modules/nf-core/sortmerna/tests/indexing_only.config' is unchanged +'modules/nf-core/sortmerna/tests/premade_index.config' is unchanged +'modules/nf-core/sortmerna/tests/tags.yml' was removed +************************************************************ diff --git a/modules/nf-core/sortmerna/tests/main.nf.test b/modules/nf-core/sortmerna/tests/main.nf.test index 1954bdfb0..4e1ced131 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test +++ b/modules/nf-core/sortmerna/tests/main.nf.test @@ -3,9 +3,12 @@ nextflow_process { name "Test Process SORTMERNA" script "../main.nf" process "SORTMERNA" + tag "modules" + tag "modules_nfcore" + tag "sortmerna" test("sarscov2 indexing only") { - + config './indexing_only.config' when { @@ -21,11 +24,17 @@ nextflow_process { } then { + def index_files = file(process.out.index[0][1]).listFiles() + .findAll { !it.name.endsWith('.stats') } + .sort { a, b -> a.name <=> b.name } + assertAll( { assert process.success }, { assert ! process.out.reads }, - { assert snapshot(process.out.index).match("index_index_only") }, - { assert snapshot(process.out.versions).match("versions_index_only") } + { assert snapshot( + index_files, + process.out.versions + ).match() }, ) } @@ -76,6 +85,10 @@ nextflow_process { } then { + def index_files = file(process.out.index[0][1]).listFiles() + .findAll { !it.name.endsWith('.stats') } + .sort { a, b -> a.name <=> b.name } + assertAll( { assert process.success }, { assert process.out.reads }, @@ -89,7 +102,7 @@ nextflow_process { ).sort() ).match("sarscov2 single_end_match") }, - { assert snapshot(process.out.index).match("index_single_end") }, + { assert snapshot(index_files).match("index_single_end") }, { assert snapshot(process.out.versions).match("versions_single_end") } ) } @@ -154,6 +167,10 @@ nextflow_process { } then { + def index_files = file(process.out.index[0][1]).listFiles() + .findAll { !it.name.endsWith('.stats') } + .sort { a, b -> a.name <=> b.name } + assertAll( { assert process.success }, { assert process.out.reads }, @@ -167,7 +184,7 @@ nextflow_process { ).sort() ).match("sarscov2 paired_end_match") }, - { assert snapshot(process.out.index).match("index_paired_end") }, + { assert snapshot(index_files).match("index_paired_end") }, { assert snapshot(process.out.versions).match("versions_paired_end") } ) } @@ -249,6 +266,10 @@ nextflow_process { } then { + def index_files = file(process.out.index[0][1]).listFiles() + .findAll { !it.name.endsWith('.stats') } + .sort { a, b -> a.name <=> b.name } + assertAll( { assert process.success }, { assert process.out.reads }, @@ -262,7 +283,7 @@ nextflow_process { ).sort() ).match("sarscov2 single_end_premade_index_match") }, - { assert snapshot(process.out.index).match("index_single_end_premade_index") }, + { assert snapshot(index_files).match("index_single_end_premade_index") }, { assert snapshot(process.out.versions).match("versions_single_end_premade_index") } ) } diff --git a/modules/nf-core/sortmerna/tests/main.nf.test.snap b/modules/nf-core/sortmerna/tests/main.nf.test.snap index 86e84733b..07c2e3294 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test.snap +++ b/modules/nf-core/sortmerna/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions_paired_end_stub": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:27:11.223149" + "timestamp": "2024-10-22T10:40:01.533875274" }, "index_paired_end_stub": { "content": [ @@ -25,34 +25,41 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T14:24:25.384097178" + "timestamp": "2024-10-22T10:40:01.450465678" }, "versions_paired_end": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:27:04.517155" + "timestamp": "2024-10-22T10:39:48.811712136" }, - "versions_single_end_stub": { + "index_only_stub": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + [ + { + "id": "test2" + }, + [ + + ] + ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-01T12:10:35.228450189" + "timestamp": "2024-10-22T10:38:56.554562414" }, "sarscov2 single_end_match": { "content": [ @@ -63,63 +70,65 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:28:23.20327" + "timestamp": "2024-10-22T10:39:09.015863183" }, - "index_only_stub": { + "versions_single_end_stub": { "content": [ [ - [ - { - "id": "test2" - }, - [ - - ] - ] + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:00:47.128504164" + "timestamp": "2024-10-22T10:39:28.573618474" }, "index_single_end_premade_index": { "content": [ [ - [ - { - "id": "test2" - }, - [ - "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" - ] - ] + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:01:53.832643452" + "timestamp": "2024-10-22T12:02:37.578808801" }, "versions_single_end_premade_index": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-22T10:40:14.269803641" + }, + "sarscov2 indexing only": { + "content": [ + [ + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" + ], + [ + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:01:53.902154982" + "timestamp": "2024-10-22T11:59:11.705138075" }, "sarscov2 paired_end-for_stub_match": { "content": [ @@ -133,32 +142,24 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:28:56.063579" + "timestamp": "2024-10-22T10:40:01.365507281" }, "index_paired_end": { "content": [ [ - [ - { - "id": "test2" - }, - [ - "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" - ] - ] + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T14:24:14.272659781" + "timestamp": "2024-10-22T12:01:29.664107565" }, "sarscov2 single_end_premade_index_match_stub": { "content": [ @@ -169,10 +170,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:05:01.913287272" + "timestamp": "2024-10-22T10:40:28.87594616" }, "sarscov2 single_end-for_stub_match": { "content": [ @@ -183,10 +184,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:28:29.197913" + "timestamp": "2024-10-22T10:39:28.458349619" }, "sarscov2 paired_end_match": { "content": [ @@ -200,46 +201,46 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:28:49.914992" + "timestamp": "2024-10-22T10:39:48.667990373" }, "versions_single_end": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T14:36:27.14244294" + "timestamp": "2024-10-22T10:39:09.110655329" }, - "versions_index_only": { + "versions_single_end_premade_index_stub": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:00:35.609161481" + "timestamp": "2024-10-22T10:40:29.097777821" }, - "versions_single_end_premade_index_stub": { + "versions_index_only_stub": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:05:02.059858431" + "timestamp": "2024-10-22T10:38:56.592840673" }, "index_single_end_stub": { "content": [ @@ -255,22 +256,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T14:23:58.068772508" - }, - "versions_index_only_stub": { - "content": [ - [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-26T15:00:47.169402699" + "timestamp": "2024-10-22T10:39:28.516407836" }, "index_single_end_premade_index_stub": { "content": [ @@ -286,54 +275,24 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:05:01.953316205" + "timestamp": "2024-10-22T10:40:28.988436085" }, "index_single_end": { "content": [ [ - [ - { - "id": "test2" - }, - [ - "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" - ] - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-26T14:36:26.88061978" - }, - "index_index_only": { - "content": [ - [ - [ - { - "id": "test2" - }, - [ - "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" - ] - ] + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:00:35.34089252" + "timestamp": "2024-10-22T12:00:30.580004574" }, "sarscov2 single_end_premade_index_match": { "content": [ @@ -344,9 +303,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:01:53.797737296" + "timestamp": "2024-10-22T10:40:14.075100849" } } \ No newline at end of file diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index e3d1c714d..7c57530a3 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::star=2.7.10a - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 + - bioconda::star=2.7.11b - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index ae67e0040..eadddb03f 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,9 +3,7 @@ process STAR_ALIGN { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" + container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(reads, stageAs: "input*/*") @@ -21,33 +19,34 @@ process STAR_ALIGN { tuple val(meta), path('*Log.progress.out'), emit: log_progress path "versions.yml" , emit: versions - tuple val(meta), path('*d.out.bam') , optional:true, emit: bam - tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted - tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript - tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted - tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq - tuple val(meta), path('*.tab') , optional:true, emit: tab - tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab - tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab - tuple val(meta), path('*.out.junction') , optional:true, emit: junction - tuple val(meta), path('*.out.sam') , optional:true, emit: sam - tuple val(meta), path('*.wig') , optional:true, emit: wig - tuple val(meta), path('*.bg') , optional:true, emit: bedgraph + tuple val(meta), path('*d.out.bam') , optional:true, emit: bam + tuple val(meta), path("${prefix}.sortedByCoord.out.bam") , optional:true, emit: bam_sorted + tuple val(meta), path("${prefix}.Aligned.sortedByCoord.out.bam") , optional:true, emit: bam_sorted_aligned + tuple val(meta), path('*toTranscriptome.out.bam') , optional:true, emit: bam_transcript + tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted + tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq + tuple val(meta), path('*.tab') , optional:true, emit: tab + tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab + tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab + tuple val(meta), path('*.out.junction') , optional:true, emit: junction + tuple val(meta), path('*.out.sam') , optional:true, emit: sam + tuple val(meta), path('*.wig') , optional:true, emit: wig + tuple val(meta), path('*.bg') , optional:true, emit: bedgraph when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def reads1 = [], reads2 = [] meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v } def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" def seq_platform = seq_platform ? "'PL:$seq_platform'" : "" def seq_center = seq_center ? "'CN:$seq_center'" : "" - def attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" + attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted' - def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' + mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' """ STAR \\ --genomeDir $index \\ @@ -79,7 +78,7 @@ process STAR_ALIGN { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ echo "" | gzip > ${prefix}.unmapped_1.fastq.gz echo "" | gzip > ${prefix}.unmapped_2.fastq.gz diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index e80dbb7dd..5cfe763e3 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -14,97 +14,212 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - index: - type: directory - description: STAR genome index - pattern: "star" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: Annotation GTF file - pattern: "*.{gtf}" - - star_ignore_sjdbgtf: - type: boolean - description: Ignore annotation GTF file - - seq_platform: - type: string - description: Sequencing platform - - seq_center: - type: string - description: Sequencing center + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - index: + type: directory + description: STAR genome index + pattern: "star" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - - star_ignore_sjdbgtf: + type: boolean + description: Ignore annotation GTF file + - - seq_platform: + type: string + description: Sequencing platform + - - seq_center: + type: string + description: Sequencing center output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - log_final: - type: file - description: STAR final log file - pattern: "*Log.final.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.final.out": + type: file + description: STAR final log file + pattern: "*Log.final.out" - log_out: - type: file - description: STAR lot out file - pattern: "*Log.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.out": + type: file + description: STAR lot out file + pattern: "*Log.out" - log_progress: - type: file - description: STAR log progress file - pattern: "*Log.progress.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.progress.out": + type: file + description: STAR log progress file + pattern: "*Log.progress.out" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*d.out.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bam_sorted: - type: file - description: Sorted BAM file of read alignments (optional) - pattern: "*sortedByCoord.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sortedByCoord.out.bam: + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*sortedByCoord.out.bam" + - bam_sorted_aligned: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.Aligned.sortedByCoord.out.bam: + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*.Aligned.sortedByCoord.out.bam" - bam_transcript: - type: file - description: Output BAM file of transcriptome alignment (optional) - pattern: "*toTranscriptome.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*toTranscriptome.out.bam": + type: file + description: Output BAM file of transcriptome alignment (optional) + pattern: "*toTranscriptome.out.bam" - bam_unsorted: - type: file - description: Unsorted BAM file of read alignments (optional) - pattern: "*Aligned.unsort.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Aligned.unsort.out.bam": + type: file + description: Unsorted BAM file of read alignments (optional) + pattern: "*Aligned.unsort.out.bam" - fastq: - type: file - description: Unmapped FastQ files (optional) - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: Unmapped FastQ files (optional) + pattern: "*fastq.gz" - tab: - type: file - description: STAR output tab file(s) (optional) - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: STAR output tab file(s) (optional) + pattern: "*.tab" + - spl_junc_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.SJ.out.tab": + type: file + description: STAR output splice junction tab file + pattern: "*.SJ.out.tab" + - read_per_gene_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ReadsPerGene.out.tab": + type: file + description: STAR output read per gene tab file + pattern: "*.ReadsPerGene.out.tab" - junction: - type: file - description: STAR chimeric junction output file (optional) - pattern: "*.out.junction" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out.junction": + type: file + description: STAR chimeric junction output file (optional) + pattern: "*.out.junction" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.out.sam" + - "*.out.sam": + type: file + description: STAR output SAM file(s) (optional) + pattern: "*.out.sam" - wig: - type: file - description: STAR output wiggle format file(s) (optional) - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" - bedgraph: - type: file - description: STAR output bedGraph format file(s) (optional) - pattern: "*.bg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bg": + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/align/star-align.diff b/modules/nf-core/star/align/star-align.diff new file mode 100644 index 000000000..ea28fb1aa --- /dev/null +++ b/modules/nf-core/star/align/star-align.diff @@ -0,0 +1,40 @@ +Changes in module 'nf-core/star/align' +Changes in 'star/align/main.nf': +--- modules/nf-core/star/align/main.nf ++++ modules/nf-core/star/align/main.nf +@@ -3,9 +3,7 @@ + label 'process_high' + + conda "${moduleDir}/environment.yml" +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : +- 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" ++ container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' + + input: + tuple val(meta), path(reads, stageAs: "input*/*") + +'modules/nf-core/star/align/meta.yml' is unchanged +'modules/nf-core/star/align/environment.yml' is unchanged +'modules/nf-core/star/align/tests/main.nf.test.snap' is unchanged +'modules/nf-core/star/align/tests/nextflow.config' is unchanged +'modules/nf-core/star/align/tests/nextflow.starfusion.config' is unchanged +'modules/nf-core/star/align/tests/nextflow.arriba.config' is unchanged +Changes in 'star/align/tests/main.nf.test': +--- modules/nf-core/star/align/tests/main.nf.test ++++ modules/nf-core/star/align/tests/main.nf.test +@@ -3,11 +3,6 @@ + name "Test Process STAR_ALIGN" + script "../main.nf" + process "STAR_ALIGN" +- tag "modules" +- tag "modules_nfcore" +- tag "star" +- tag "star/align" +- tag "star/genomegenerate" + + test("homo_sapiens - single_end") { + config "./nextflow.config" + +'modules/nf-core/star/align/tests/tags.yml' was removed +************************************************************ diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 69f655ef4..2fa21352e 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -51,13 +51,10 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -119,13 +116,10 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -187,13 +181,9 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + bam(process.out.bam[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -255,13 +245,10 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + file(process.out.junction[0][1]).name, + bam(process.out.bam[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -325,13 +312,10 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -601,4 +585,4 @@ nextflow_process { ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap index c814eb56c..b533fb8b4 100644 --- a/modules/nf-core/star/align/tests/main.nf.test.snap +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -26,7 +26,11 @@ "id": "test", "single_end": true }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -35,7 +39,7 @@ "id": "test", "single_end": true }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -44,7 +48,7 @@ "id": "test", "single_end": true }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -53,7 +57,7 @@ "id": "test", "single_end": true }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -62,10 +66,19 @@ "id": "test", "single_end": true }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -84,7 +97,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -105,10 +118,7 @@ "id": "test", "single_end": true }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -117,7 +127,7 @@ "id": "test", "single_end": true }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -126,7 +136,7 @@ "id": "test", "single_end": true }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -135,10 +145,7 @@ "id": "test", "single_end": true }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -148,9 +155,8 @@ "single_end": true }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -173,10 +179,16 @@ "id": "test", "single_end": true }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -295,7 +307,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -310,9 +322,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:16:04.712114" + "timestamp": "2024-10-20T17:09:08.738074176" }, "homo_sapiens - paired_end - arriba - stub": { "content": [ @@ -341,7 +353,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -350,7 +366,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -359,7 +375,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -368,7 +384,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -377,10 +393,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -399,7 +424,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -420,10 +445,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -432,7 +454,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -441,7 +463,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -450,10 +472,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -463,9 +482,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -488,10 +506,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -610,7 +634,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -625,39 +649,17 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:16:28.874293" + "timestamp": "2024-10-20T17:09:36.122131869" }, "homo_sapiens - single_end": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": true - }, - "test.Aligned.sortedByCoord.out.bam:md5,c6cfaccaf91bc7fdabed3cfe236d4535" - ] - ], - [ - [ - { - "id": "test", - "single_end": true - }, - "test.Aligned.sortedByCoord.out.bam:md5,c6cfaccaf91bc7fdabed3cfe236d4535" - ] - ], - [ - - ], - [ - - ], + "9f76be49a6607613a64f760101bdddce", + "9f76be49a6607613a64f760101bdddce", [ [ { @@ -678,9 +680,6 @@ ], [ - ], - [ - ], [ [ @@ -704,44 +703,22 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T18:02:34.35338" + "timestamp": "2024-10-20T17:01:22.197991909" }, "homo_sapiens - paired_end": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" - ] - ], - [ - - ], - [ - - ], + "db9a8324b5163b025bcc0c33e848486", + "db9a8324b5163b025bcc0c33e848486", [ [ { @@ -762,9 +739,6 @@ ], [ - ], - [ - ], [ [ @@ -788,14 +762,14 @@ ], [ - 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"test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -860,10 +838,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -882,7 +869,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -903,10 +890,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -915,7 +899,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -924,7 +908,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -933,10 +917,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -946,9 +927,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -971,10 +951,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1093,7 +1079,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -1108,39 +1094,17 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:16:51.360287" + "timestamp": "2024-10-20T17:10:12.005468781" }, "homo_sapiens - paired_end - multiple": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" - ] - ], - [ - - ], - [ - - ], + "3e54e45f5dc3e9c1f2fc55bc41531a87", + "3e54e45f5dc3e9c1f2fc55bc41531a87", [ [ { @@ -1161,9 +1125,6 @@ ], [ - ], - [ - ], [ [ @@ -1187,14 +1148,14 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T13:13:28.987438" + "timestamp": "2024-10-20T17:08:54.877286681" }, "homo_sapiens - paired_end - stub": { "content": [ @@ -1223,7 +1184,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -1232,7 +1197,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -1241,7 +1206,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -1250,7 +1215,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -1259,10 +1224,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -1281,7 +1255,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -1302,10 +1276,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -1314,7 +1285,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -1323,7 +1294,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -1332,10 +1303,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -1345,9 +1313,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1370,10 +1337,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1492,7 +1465,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -1507,27 +1480,17 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:16:16.798018" + "timestamp": "2024-10-20T17:09:20.911466345" }, "homo_sapiens - paired_end - starfusion": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.out.bam:md5,bcad07b838f6762fc01eea52b5cd3f84" - ] - ], - [ - - ], + "test.Chimeric.out.junction", + "caee9dcda13882d4913456973c25b57a", [ ], @@ -1539,21 +1502,6 @@ ], [ - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Chimeric.out.junction:md5,c10ef219f4a30e83711b995bc5e40dba" - ] - ], - [ - - ], - [ - ], [ [ @@ -1577,41 +1525,21 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T13:10:55.371956" + "timestamp": "2024-10-20T17:07:25.0639914" }, "homo_sapiens - paired_end - arriba": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5" - ] - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], + "1a3abe88fb2490589c58497d39921bcc", [ ], @@ -1646,14 +1574,14 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T13:05:10.7534" + "timestamp": "2024-10-20T17:04:00.685784211" }, "homo_sapiens - paired_end - starfusion - stub": { "content": [ @@ -1682,7 +1610,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -1691,7 +1623,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -1700,7 +1632,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -1709,7 +1641,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -1718,10 +1650,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -1740,7 +1681,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -1761,10 +1702,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -1773,7 +1711,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -1782,7 +1720,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -1791,10 +1729,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -1804,9 +1739,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1829,10 +1763,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1951,7 +1891,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -1966,8 +1906,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:16:40.64399" + "timestamp": "2024-10-20T17:09:53.173671551" } } \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config index 2324b9e58..cf09323fc 100644 --- a/modules/nf-core/star/align/tests/nextflow.arriba.config +++ b/modules/nf-core/star/align/tests/nextflow.arriba.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config index c4ac58088..18bc2ee8a 100644 --- a/modules/nf-core/star/align/tests/nextflow.config +++ b/modules/nf-core/star/align/tests/nextflow.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config index 467b64977..7880bfcf5 100644 --- a/modules/nf-core/star/align/tests/nextflow.starfusion.config +++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 38611dfa2..7c57530a3 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 - - bioconda::star=2.7.10a + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 + - bioconda::star=2.7.11b - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index b8855715b..af72f920b 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,9 +3,7 @@ process STAR_GENOMEGENERATE { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" + container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index 1061e1b8d..33c1f65f3 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -14,37 +14,40 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of the reference genome - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the reference genome + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: directory - description: Folder containing the star index files - pattern: "star" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - star: + type: directory + description: Folder containing the star index files + pattern: "star" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff new file mode 100644 index 000000000..dea48619b --- /dev/null +++ b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff @@ -0,0 +1,36 @@ +Changes in module 'nf-core/star/genomegenerate' +Changes in 'star/genomegenerate/main.nf': +--- modules/nf-core/star/genomegenerate/main.nf ++++ modules/nf-core/star/genomegenerate/main.nf +@@ -3,9 +3,7 @@ + label 'process_high' + + conda "${moduleDir}/environment.yml" +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : +- 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" ++ container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' + + input: + tuple val(meta), path(fasta) + +'modules/nf-core/star/genomegenerate/meta.yml' is unchanged +'modules/nf-core/star/genomegenerate/environment.yml' is unchanged +'modules/nf-core/star/genomegenerate/tests/main.nf.test.snap' is unchanged +Changes in 'star/genomegenerate/tests/main.nf.test': +--- modules/nf-core/star/genomegenerate/tests/main.nf.test ++++ modules/nf-core/star/genomegenerate/tests/main.nf.test +@@ -3,10 +3,6 @@ + name "Test Process STAR_GENOMEGENERATE" + script "../main.nf" + process "STAR_GENOMEGENERATE" +- tag "modules" +- tag "modules_nfcore" +- tag "star" +- tag "star/genomegenerate" + + test("fasta_gtf") { + + +'modules/nf-core/star/genomegenerate/tests/tags.yml' was removed +************************************************************ diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap index 207f4b4f5..3db256782 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]", [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:55:35.478401" + "timestamp": "2024-10-19T20:37:47.410432728" }, "fasta_gtf_stub": { "content": [ @@ -41,7 +41,7 @@ ] ], "1": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ], "index": [ [ @@ -69,15 +69,15 @@ ] ], "versions": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:55:57.247585" + "timestamp": "2024-10-19T20:38:09.165234795" }, "fasta_stub": { "content": [ @@ -101,7 +101,7 @@ ] ], "1": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ], "index": [ [ @@ -122,27 +122,27 @@ ] ], "versions": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:56:07.01742" + "timestamp": "2024-10-19T20:38:19.530862664" }, "fasta": { "content": [ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]", [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:55:45.48784" + "timestamp": "2024-10-19T20:37:58.667436398" } } \ No newline at end of file diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 0556de41a..906b7486c 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::stringtie=2.2.1 + - bioconda::stringtie=2.2.3 diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 6e25ba27d..4635c8c5b 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -4,8 +4,8 @@ process STRINGTIE_STRINGTIE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'biocontainers/stringtie:2.2.1--hecb563c_2' }" + 'https://depot.galaxyproject.org/singularity/stringtie:2.2.3--h43eeafb_0' : + 'biocontainers/stringtie:2.2.3--h43eeafb_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/stringtie/stringtie/meta.yml b/modules/nf-core/stringtie/stringtie/meta.yml index d8ebdd88a..e55b2abfc 100644 --- a/modules/nf-core/stringtie/stringtie/meta.yml +++ b/modules/nf-core/stringtie/stringtie/meta.yml @@ -12,46 +12,67 @@ tools: homepage: https://ccb.jhu.edu/software/stringtie/index.shtml documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual licence: ["MIT"] + identifier: biotools:stringtie input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - Stringtie transcript gtf output(s). - - annotation_gtf: - type: file - description: | - Annotation gtf file (optional). + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + Stringtie transcript gtf output(s). + - - annotation_gtf: + type: file + description: | + Annotation gtf file (optional). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - transcript_gtf: - type: file - description: transcript gtf - pattern: "*.{transcripts.gtf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.gtf": + type: file + description: transcript gtf + pattern: "*.{transcripts.gtf}" + - abundance: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.abundance.txt": + type: file + description: abundance + pattern: "*.{abundance.txt}" - coverage_gtf: - type: file - description: coverage gtf - pattern: "*.{coverage.gtf}" - - abudance: - type: file - description: abudance - pattern: "*.{abudance.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.coverage.gtf": + type: file + description: coverage gtf + pattern: "*.{coverage.gtf}" - ballgown: - type: file - description: for running ballgown - pattern: "*.{ballgown}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ballgown": + type: file + description: for running ballgown + pattern: "*.{ballgown}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap index 124dd4cbe..d4645de3e 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap @@ -31,18 +31,18 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" + "test.transcripts.gtf:md5,37154e7bda96544f24506ee902bb561d" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:44.299962" + "timestamp": "2024-10-18T09:56:50.294157199" }, "sarscov2 [bam] - forward strandedness": { "content": [ @@ -61,18 +61,18 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" + "test.transcripts.gtf:md5,6087dfc9700a52d9e4a1ae3fcd1d1dfd" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:35.177738" + "timestamp": "2024-10-18T09:56:39.4249133" }, "sarscov2 [bam] - forward strandedness - stub": { "content": [ @@ -114,7 +114,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -153,15 +153,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:32.885078" + "timestamp": "2024-10-18T09:57:23.008470065" }, "sarscov2 [bam] - forward strandedness + reference annotation - stub": { "content": [ @@ -203,7 +203,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -242,15 +242,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:43.325777" + "timestamp": "2024-10-18T09:57:33.622824981" }, "sarscov2 [bam] - reverse strandedness + reference annotation - stub": { "content": [ @@ -292,7 +292,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -331,15 +331,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:37:06.085936" + "timestamp": "2024-10-18T09:57:55.803421433" }, "sarscov2 [bam] - reverse strandedness - stub": { "content": [ @@ -381,7 +381,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -420,15 +420,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:53.837578" + "timestamp": "2024-10-18T09:57:44.825389635" }, "sarscov2 [bam] - reverse strandedness + reference annotation": { "content": [ @@ -462,18 +462,18 @@ "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" + "test.transcripts.gtf:md5,fbabb4e3888bbede67f11f692e484880" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:34:03.114695" + "timestamp": "2024-10-18T09:57:11.793664242" }, "sarscov2 [bam] - reverse strandedness": { "content": [ @@ -492,17 +492,17 @@ "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" + "test.transcripts.gtf:md5,01d6da00a3c458420841e57427297183" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:52.874479" + "timestamp": "2024-10-18T09:57:01.166309777" } } \ No newline at end of file diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 7e919aa31..fdb575020 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::subread=2.0.1 + - bioconda::subread=2.0.6 diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 471bd16fd..d51de1e0b 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -4,8 +4,8 @@ process SUBREAD_FEATURECOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : - 'biocontainers/subread:2.0.1--hed695b0_0' }" + 'https://depot.galaxyproject.org/singularity/subread:2.0.6--he4a0461_2' : + 'biocontainers/subread:2.0.6--he4a0461_2' }" input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/subread/featurecounts/meta.yml b/modules/nf-core/subread/featurecounts/meta.yml index 38a379456..a9b045b7d 100644 --- a/modules/nf-core/subread/featurecounts/meta.yml +++ b/modules/nf-core/subread/featurecounts/meta.yml @@ -7,43 +7,55 @@ keywords: - reference tools: - featurecounts: - description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads. + description: featureCounts is a highly efficient general-purpose read summarization + program that counts mapped reads for genomic features such as genes, exons, + promoter, gene bodies, genomic bins and chromosomal locations. It can be used + to count both RNA-seq and genomic DNA-seq reads. homepage: http://bioinf.wehi.edu.au/featureCounts/ documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf doi: "10.1093/bioinformatics/btt656" licence: ["GPL v3"] + identifier: biotools:subread input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file containing read alignments - pattern: "*.{bam}" - - annotation: - type: file - description: Genomic features annotation in GTF or SAF - pattern: "*.{gtf,saf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: BAM files containing mapped reads + pattern: "*.bam" + - annotation: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf,saf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - counts: - type: file - description: Counts of reads mapping to features - pattern: "*featureCounts.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt": + type: file + description: Counts of reads mapping to features + pattern: "*featureCounts.txt" - summary: - type: file - description: Summary log file - pattern: "*.featureCounts.txt.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt.summary": + type: file + description: Summary log file + pattern: "*.featureCounts.txt.summary" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap index 72e8dcddf..5a743f0ce 100644 --- a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap @@ -8,15 +8,15 @@ "single_end": true, "strandedness": "forward" }, - "test.featureCounts.txt:md5,0012df4c0a0e47eec1440017ab34f75f" + "test.featureCounts.txt:md5,4cf89f0e702ba9abef3fa571e68fe8f0" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:10.685863663" + "timestamp": "2024-10-18T10:19:47.695388295" }, "unstranded_counts": { "content": [ @@ -27,15 +27,15 @@ "single_end": true, "strandedness": "unstranded" }, - "test.featureCounts.txt:md5,3307d31b44a5d6bb3389786bb8f4e91f" + "test.featureCounts.txt:md5,c4ef2c2a80547fbb3074331bc0a1bda3" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:38.67903701" + "timestamp": "2024-10-18T10:21:03.208334705" }, "reverse_summary": { "content": [ @@ -80,7 +80,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -103,15 +103,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:04:22.628032" + "timestamp": "2024-10-18T10:20:10.040191252" }, "sarscov2 [bam] - reverse - stub": { "content": [ @@ -137,7 +137,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -160,15 +160,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:04:52.371212" + "timestamp": "2024-10-18T10:20:42.708101743" }, "reverse_counts": { "content": [ @@ -179,15 +179,15 @@ "single_end": true, "strandedness": "reverse" }, - "test.featureCounts.txt:md5,8175816b8260ed444d59232bd7e7120b" + "test.featureCounts.txt:md5,a7d8843ebc12d855c2e68d3e2e137582" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:25.160010804" + "timestamp": "2024-10-18T10:20:24.490755916" }, "sarscov2 [bam] - unstranded - stub": { "content": [ @@ -213,7 +213,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -236,15 +236,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:05:25.058902" + "timestamp": "2024-10-18T10:21:19.244837771" }, "forward_summary": { "content": [ @@ -268,14 +268,14 @@ "forward_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:10.704797013" + "timestamp": "2024-10-18T10:19:48.001158764" }, "unstranded_summary": { "content": [ @@ -299,25 +299,25 @@ "reverse_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:25.175265594" + "timestamp": "2024-10-18T10:20:24.551053149" }, "unstranded_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:38.69390501" + "timestamp": "2024-10-18T10:21:03.25895568" } } \ No newline at end of file diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml index e5118d289..820d4f163 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "summarizedexperiment_summarizedexperiment" description: | @@ -11,68 +10,77 @@ keywords: - assay tools: - "summarizedexperiment": - description: "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples." + description: "The SummarizedExperiment container contains one or more assays, + each represented by a matrix-like object of numeric or other mode. The rows + typically represent genomic ranges of interest and the columns represent samples." homepage: "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html" tool_dev_url: "https://github.com/Bioconductor/SummarizedExperiment" doi: "10.18129/B9.bioc.SummarizedExperiment" licence: ["Artistic-2.0"] + identifier: biotools:summarizedexperiment input: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - matrix_files: - type: directory - description: | - One or more paths to CSV or TSV matrix files. All files must have the - same rows and columns. - pattern: "*.{csv,tsv}" - - meta2: - type: map - description: | - Groovy Map containing reference information related to the species - reference from which matrix rows are derived e.g. `[ id:'yeast' ]` - - rowdata: - type: file - description: | - Metadata on matrix features. One column must contain all matrix row - IDs. - pattern: "*.{csv,tsv}" - - meta3: - type: map - description: | - Groovy Map containing information related to the experiment as a whole, - as represented by the matrix columns and the sample sheet e.g. - `[id:'SRP123456' ]` - - coldata: - type: file - description: | - Metadata on matrix columns. One column must contain all matrix column - IDs. - pattern: "*.{csv,tsv}" - + - - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - matrix_files: + type: directory + description: | + One or more paths to CSV or TSV matrix files. All files must have the + same rows and columns. + pattern: "*.{csv,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference from which matrix rows are derived e.g. `[ id:'yeast' ]` + - rowdata: + type: file + description: | + Metadata on matrix features. One column must contain all matrix row + IDs. + pattern: "*.{csv,tsv}" + - - meta3: + type: map + description: | + Groovy Map containing information related to the experiment as a whole, + as represented by the matrix columns and the sample sheet e.g. + `[id:'SRP123456' ]` + - coldata: + type: file + description: | + Metadata on matrix columns. One column must contain all matrix column + IDs. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - rds: - type: file - description: Serialised SummarizedExperiment object - pattern: "*.SummarizedExperiment.rds" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*.rds": + type: file + description: Serialised SummarizedExperiment object + pattern: "*.SummarizedExperiment.rds" - log: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test index 8faa18afb..f80f3ee44 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT" + setup { run("UNTAR") { diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index f172c1b39..622407eda 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::cutadapt=3.4 - - bioconda::trim-galore=0.6.7 + - bioconda::cutadapt=4.9 + - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 0e2f32902..8a2fc54b3 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,8 +4,8 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.7--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 6cb31c9f9..21da84933 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "test_trimgalore_single_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:20.401347" + "timestamp": "2024-10-22T19:23:17.969056957" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +42,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "html": [ @@ -69,7 +69,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "zip": [ @@ -77,10 +77,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:27:44.964166" + "timestamp": "2024-10-22T19:23:28.617831159" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +119,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "html": [ @@ -152,7 +152,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "zip": [ @@ -160,21 +160,21 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:28:07.611496" + "timestamp": "2024-10-22T19:23:51.539787731" }, "test_trimgalore_paired_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:28.960497" + "timestamp": "2024-10-22T19:23:41.16485915" } } \ No newline at end of file diff --git a/modules/nf-core/tximeta/tximport/meta.yml b/modules/nf-core/tximeta/tximport/meta.yml index 9ee5fd365..d4c6a5492 100644 --- a/modules/nf-core/tximeta/tximport/meta.yml +++ b/modules/nf-core/tximeta/tximport/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tximeta_tximport" description: | @@ -18,102 +17,131 @@ tools: tool_dev_url: "https://github.com/thelovelab/tximeta" doi: "10.1371/journal.pcbi.1007664" licence: ["GPL-2"] + identifier: biotools:tximeta input: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - quants: - type: directory - description: Paths to subdirectories corresponding to - sample-wise runs of Salmon or Kallisto - - meta2: - type: map - description: | - Groovy Map containing reference information related to the species - reference e.g. `[ id:'yeast' ]` - - tx2gene: - type: file - description: A transcript to gene mapping table such as those generated - by custom/tx2gene - pattern: "*.{csv,tsv}" - - meta3: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - coldata: - type: file - description: | - Optional 'coldata' file equivalent to a sample sheet where the first - column corresponds to the sample names (directory names in the input - salmon/ kallisto results) - pattern: "*.{csv,tsv}" - - quant_type: - type: string - description: Quantification type, 'kallisto' or 'salmon' - + - - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - '"quants/*"': + type: directory + description: Directory containing quantification files + - - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference e.g. `[ id:'yeast' ]` + - tx2gene: + type: file + description: A transcript to gene mapping table such as those generated by custom/tx2gene + pattern: "*.{csv,tsv}" + - - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' output: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - tpm_gene: - type: file - description: | - Abundance (TPM) values derived from tximport output after - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*gene_tpm.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_tpm.tsv": + type: file + description: | + Abundance (TPM) values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_tpm.tsv" - counts_gene: - type: file - description: | - Count values derived from tximport output after - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*gene_counts.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts.tsv": + type: file + description: | + Count values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_counts.tsv" - counts_gene_length_scaled: - type: file - description: | - Count values derived from tximport output after summarizeToGene(), with - a 'countsFromAbundance' specification of 'lengthScaledTPM' - pattern: "*gene_counts_length_scaled.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts_length_scaled.tsv": + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'lengthScaledTPM' + pattern: "*gene_counts_length_scaled.tsv" - counts_gene_scaled: - type: file - description: | - Count values derived from tximport output after summarizeToGene(), with - a 'countsFromAbundance' specification of 'scaledTPM' - pattern: "*gene_counts_scaled.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts_scaled.tsv": + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'scaledTPM' + pattern: "*gene_counts_scaled.tsv" - lengths_gene: - type: file - description: | - Length values derived from tximport output after summarizeToGene(), - without a 'countsFromAbundance' specification - pattern: "*gene_lengths.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_lengths.tsv": + type: file + description: | + Length values derived from tximport output after summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" - tpm_transcript: - type: file - description: | - Abundance (TPM) values derived from tximport output without - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*transcript_tpm.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_tpm.tsv": + type: file + description: | + Abundance (TPM) values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_tpm.tsv" - counts_transcript: - type: file - description: | - Count values derived from tximport output without - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*transcript_counts.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_counts.tsv": + type: file + description: | + Count values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_counts.tsv" - lengths_transcript: - type: file - description: | - Length values derived from tximport output without summarizeToGene(), - without a 'countsFromAbundance' specification - pattern: "*gene_lengths.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_lengths.tsv": + type: file + description: | + Length values derived from tximport output without summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ucsc/bedclip/meta.yml b/modules/nf-core/ucsc/bedclip/meta.yml index 2467a28f2..9222d31d2 100644 --- a/modules/nf-core/ucsc/bedclip/meta.yml +++ b/modules/nf-core/ucsc/bedclip/meta.yml @@ -9,30 +9,36 @@ tools: description: Remove lines from bed file that refer to off-chromosome locations. homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedgraph}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: bedGraph file + pattern: "*.{bedgraph}" + - - sizes: + type: file + description: Chromosome sizes file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedgraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph": + type: file + description: bedGraph file + pattern: "*.{bedgraph}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index a54fb8f16..27868a444 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedgraphtobigwig=445 + - bioconda::ucsc-bedgraphtobigwig=469 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index bff0b00a9..81cdee953 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -5,8 +5,8 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:445--h954228d_0' : - 'biocontainers/ucsc-bedgraphtobigwig:445--h954228d_0' }" + 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:469--h9b8f530_0' : + 'biocontainers/ucsc-bedgraphtobigwig:469--h9b8f530_0' }" input: tuple val(meta), path(bedgraph) @@ -22,7 +22,7 @@ process UCSC_BEDGRAPHTOBIGWIG { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '469' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ bedGraphToBigWig \\ $bedgraph \\ @@ -37,7 +37,7 @@ process UCSC_BEDGRAPHTOBIGWIG { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '469' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.bigWig diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml index a60118abe..5d42cbde7 100755 --- a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml @@ -12,34 +12,37 @@ tools: homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ documentation: https://genome.ucsc.edu/goldenPath/help/bigWig.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedGraph}" - - sizes: - type: file - description: chromosome sizes file - pattern: "*.{sizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: bedGraph file + pattern: "*.{bedGraph}" + - - sizes: + type: file + description: chromosome sizes file + pattern: "*.{sizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bigwig: - type: file - description: bigWig file - pattern: "*.{bigWig}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bigWig": + type: file + description: bigWig file + pattern: "*.{bigWig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap index 7b0181583..7c731f651 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ], "bigwig": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:06:05.176746" + "timestamp": "2024-10-18T10:47:58.558813949" }, "Should run without failures": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ], "bigwig": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:05:56.658148" + "timestamp": "2024-10-18T10:47:36.476844229" } } \ No newline at end of file diff --git a/modules/nf-core/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml index 38d3fd465..6cbd84116 100644 --- a/modules/nf-core/umitools/dedup/meta.yml +++ b/modules/nf-core/umitools/dedup/meta.yml @@ -1,5 +1,6 @@ name: umitools_dedup -description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. +description: Deduplicate reads based on the mapping co-ordinate and the UMI attached + to the read. keywords: - umitools - deduplication @@ -7,60 +8,89 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" - - get_output_stats: - type: boolean - description: | - Whether or not to generate output stats. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" + - - get_output_stats: + type: boolean + description: | + Whether or not to generate output stats. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with deduplicated UMIs. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file with deduplicated UMIs. + pattern: "*.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" - tsv_edit_distance: - type: file - description: Reports the (binned) average edit distance between the UMIs at each position. - pattern: "*edit_distance.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*edit_distance.tsv": + type: file + description: Reports the (binned) average edit distance between the UMIs at + each position. + pattern: "*edit_distance.tsv" - tsv_per_umi: - type: file - description: UMI-level summary statistics. - pattern: "*per_umi.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*per_umi.tsv": + type: file + description: UMI-level summary statistics. + pattern: "*per_umi.tsv" - tsv_umi_per_position: - type: file - description: Tabulates the counts for unique combinations of UMI and position. - pattern: "*per_position.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*per_position.tsv": + type: file + description: Tabulates the counts for unique combinations of UMI and position. + pattern: "*per_position.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/umitools/prepareforrsem/meta.yml b/modules/nf-core/umitools/prepareforrsem/meta.yml index 8b85366cc..3e8ead257 100644 --- a/modules/nf-core/umitools/prepareforrsem/meta.yml +++ b/modules/nf-core/umitools/prepareforrsem/meta.yml @@ -8,43 +8,53 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Prepared BAM file. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Prepared BAM file. + pattern: "*.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@pinin4fjords" diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index a9a2110f5..290346b3f 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -10,30 +10,33 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - untar: - type: directory - description: Directory containing contents of archive - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - $prefix: + type: directory + description: Directory containing contents of archive + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/nextflow.config b/nextflow.config index 496a9429f..468792d0f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -186,6 +186,7 @@ profiles { } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + includeConfig 'conf/arm.config' } singularity { singularity.enabled = true @@ -327,7 +328,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '3.16.1' + version = '3.17.0' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 511ff6e63..106710e05 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -1,36 +1,55 @@ +def generateStarAlignArgs(save_unaligned, contaminant_screening, extra_star_align_args) { + def argsToMap = { String args -> + args.split(/\s(?=--)/).collectEntries { + def parts = it.trim().split(/\s+/, 2) + [(parts[0]): parts.size() > 1 ? parts[1] : ''] + } + } + + def base_args = """ + --quantMode TranscriptomeSAM + --twopassMode Basic + --outSAMtype BAM Unsorted + --readFilesCommand zcat + --runRNGseed 0 + --outFilterMultimapNmax 20 + --alignSJDBoverhangMin 1 + --outSAMattributes NH HI AS NM MD + --outSAMstrandField intronMotif + """.trim() + + if (save_unaligned || contaminant_screening) { + base_args += "\n--outReadsUnmapped Fastx" + } + + def final_args_map = argsToMap(base_args) + (extra_star_align_args ? argsToMap(extra_star_align_args) : [:]) + final_args_map.collect { key, value -> "${key} ${value}".trim() }.join(' ') +} + if (!params.skip_alignment && params.aligner == 'star_salmon') { process { - withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - ext.args = { - // Function to convert argument strings into a map - def argsToMap = { String args -> - args.split("\\s(?=--)").collectEntries { - def parts = it.trim().split(/\s+/, 2) - [(parts.first()): parts.last()] - } - } - - // Initialize the map with preconfigured values - def preset_args_map = argsToMap(""" - --quantMode TranscriptomeSAM - --twopassMode Basic - --outSAMtype BAM Unsorted - --readFilesCommand zcat - --runRNGseed 0 - --outFilterMultimapNmax 20 - --alignSJDBoverhangMin 1 - --outSAMattributes NH HI AS NM MD - --quantTranscriptomeBan Singleend - --outSAMstrandField intronMotif - ${params.save_unaligned || params.contaminant_screening ? '--outReadsUnmapped Fastx' : ''} - """.trim()) - // Consolidate the extra arguments - def final_args_map = preset_args_map + (params.extra_star_align_args ? argsToMap(params.extra_star_align_args) : [:]) + // We have to condition this, because the args are slightly different between the latest STAR and the one compatible with iGenomes - // Convert the map back to a list and then to a single string - final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim() + withName: '.*:ALIGN_STAR:STAR_ALIGN' { + ext.args = { + generateStarAlignArgs( + params.save_unaligned, + params.contaminant_screening, + (params.extra_star_align_args ?: '') + ' --quantTranscriptomeSAMoutput BanSingleEnd' + ) + } + } + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + ext.args = { + generateStarAlignArgs( + params.save_unaligned, + params.contaminant_screening, + (params.extra_star_align_args ?: '') + ' --quantTranscriptomeBan Singleend' + ) } + } + withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { publishDir = [ [ diff --git a/subworkflows/local/align_star/tests/main.nf.test.snap b/subworkflows/local/align_star/tests/main.nf.test.snap index e3a4b2e03..b8224b7fd 100644 --- a/subworkflows/local/align_star/tests/main.nf.test.snap +++ b/subworkflows/local/align_star/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "id": "test", "single_end": false }, - "test.bam.bai:md5,8bfbd4094a92ac0de8492d98a471d1b0" + "test.bam.bai:md5,4cf31974d82bed533f4b6528dff95b50" ] ], [ @@ -18,7 +18,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,fc154c31eb4d034ebdb6b1d17c6b45eb" + "test.bam:md5,7137528dd300c4ae0f7e3370a5555c79" ] ], [ @@ -81,7 +81,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,202e2f234f93b347b6a72d0163773054" + "test.stats:md5,bad7f610455554f5523eb1ae58ab7afe" ] ], [ @@ -94,19 +94,19 @@ ] ], [ - "versions.yml:md5,06693106908e6f8f38a2c30accf7067d", - "versions.yml:md5,369619588c8c294b74dca9058a151b11", - "versions.yml:md5,78069d4515b04251f758ac52a49d9971", - "versions.yml:md5,b6a22ef369a375445a8f9313721b8092", - "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc", - "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434" + "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", + "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", + "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", + "versions.yml:md5,d5e8b4d761dd85a303814239077bd666", + "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T19:13:41.194686" + "timestamp": "2024-10-21T14:53:32.322441137" }, "star - no igenomes - stub": { "content": [ @@ -134,10 +134,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -233,19 +230,19 @@ ] ], [ - "versions.yml:md5,06693106908e6f8f38a2c30accf7067d", - "versions.yml:md5,35c1cc21d26d9d8f00e6ec87e97fb634", - "versions.yml:md5,369619588c8c294b74dca9058a151b11", - "versions.yml:md5,78069d4515b04251f758ac52a49d9971", - "versions.yml:md5,b6a22ef369a375445a8f9313721b8092", - "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434" + "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,708098dd31c984730b066ead621a33f7", + "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", + "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", + "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", + "versions.yml:md5,d5e8b4d761dd85a303814239077bd666" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:43:30.675108" + "timestamp": "2024-10-21T20:42:29.835710637" }, "star - no igenomes": { "content": [ @@ -257,7 +254,7 @@ "id": "test", "single_end": false }, - "test.bam.bai:md5,8bfbd4094a92ac0de8492d98a471d1b0" + "test.bam.bai:md5,59e8552f0e50c540d41198496bf34251" ] ], [ @@ -266,17 +263,11 @@ "id": "test", "single_end": false }, - "test.bam:md5,e6573d093da6ec95f99c1669eb86bbd6" + "test.bam:md5,0d47a5f971c1548eadc1f3c39dab0dbf" ] ], [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" - ] + ], [ @@ -320,7 +311,7 @@ "id": "test", "single_end": false }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" + "test.Aligned.sortedByCoord.out.bam:md5,4e917b4befbbe216fd666d06af0298af" ] ], [ @@ -329,7 +320,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,202e2f234f93b347b6a72d0163773054" + "test.stats:md5,bad7f610455554f5523eb1ae58ab7afe" ] ], [ @@ -342,19 +333,19 @@ ] ], [ - "versions.yml:md5,06693106908e6f8f38a2c30accf7067d", - "versions.yml:md5,35c1cc21d26d9d8f00e6ec87e97fb634", - "versions.yml:md5,369619588c8c294b74dca9058a151b11", - "versions.yml:md5,78069d4515b04251f758ac52a49d9971", - "versions.yml:md5,b6a22ef369a375445a8f9313721b8092", - "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434" + "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,708098dd31c984730b066ead621a33f7", + "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", + "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", + "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", + "versions.yml:md5,d5e8b4d761dd85a303814239077bd666" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T19:12:49.496188" + "timestamp": "2024-10-21T20:40:55.299198285" }, "star - with igenomes - stub": { "content": [ @@ -481,18 +472,18 @@ ] ], [ - "versions.yml:md5,06693106908e6f8f38a2c30accf7067d", - "versions.yml:md5,369619588c8c294b74dca9058a151b11", - "versions.yml:md5,78069d4515b04251f758ac52a49d9971", - "versions.yml:md5,b6a22ef369a375445a8f9313721b8092", - "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc", - "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434" + "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", + "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", + "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", + "versions.yml:md5,d5e8b4d761dd85a303814239077bd666", + "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:43:56.680384" + "timestamp": "2024-10-21T14:54:32.959245404" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap index 88d78c211..f5c0a10f7 100644 --- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap @@ -41,17 +41,17 @@ "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta" ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T17:03:34.032908" + "timestamp": "2024-10-21T14:42:50.037244182" }, "skip_pseudo_alignment - stub": { "content": [ @@ -95,18 +95,18 @@ "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta" ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T16:59:05.328944" + "timestamp": "2024-10-21T14:36:51.108422744" }, "skip_gtf_filter": { "content": [ @@ -150,17 +150,17 @@ ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", - "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5", + "versions.yml:md5,04400316552e6253e0008f052b20d866", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", - "versions.yml:md5,bc99889446f02427c166b3219b793672" + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T19:15:45.003106" + "timestamp": "2024-10-21T14:21:35.428370538" }, "gencode = false - stub": { "content": [ @@ -204,18 +204,18 @@ "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta" ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T16:57:20.218814" + "timestamp": "2024-10-21T14:34:45.22576799" }, "gff = false - stub": { "content": [ @@ -259,18 +259,18 @@ "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta" ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - 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"timestamp": "2024-07-03T19:17:45.167724" + "timestamp": "2024-10-21T14:24:29.339763401" }, "default options - stub": { "content": [ @@ -1802,18 +1802,18 @@ "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta" ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T16:56:58.012938" + "timestamp": "2024-10-21T14:34:12.631669075" }, "salmon_index = false": { "content": [ @@ -1857,18 +1857,18 @@ ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", - "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5", + "versions.yml:md5,04400316552e6253e0008f052b20d866", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672" + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T19:19:42.999843" + "timestamp": "2024-10-21T14:28:32.12627675" }, "rsem_index = false": { "content": [ @@ -1912,18 +1912,18 @@ ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", - "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5", + "versions.yml:md5,04400316552e6253e0008f052b20d866", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672" + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - 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stub": { "content": [ @@ -2022,19 +2022,19 @@ "genome.transcripts.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", "versions.yml:md5,918fe0b59c0986eb602ace85841c5ab3", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T17:00:43.920677" + "timestamp": "2024-10-21T14:38:52.064137724" }, "skip_alignment = true": { "content": [ @@ -2078,18 +2078,18 @@ ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", - "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5", + "versions.yml:md5,04400316552e6253e0008f052b20d866", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672" + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T19:22:08.9618" + "timestamp": "2024-10-21T14:32:57.856332379" }, "skip_gtf_filter = true": { "content": [ @@ -2133,17 +2133,17 @@ ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", - "versions.yml:md5,1cd265cb86a23a27f683ffb2459f37f5", + "versions.yml:md5,04400316552e6253e0008f052b20d866", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", - "versions.yml:md5,bc99889446f02427c166b3219b793672" + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T19:21:18.583526" + "timestamp": "2024-10-21T14:31:25.686724069" }, "hisat2_index = false - stub": { "content": [ @@ -2187,18 +2187,18 @@ "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta" ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T17:02:19.539518" + "timestamp": "2024-10-21T14:40:52.285127199" }, "skip_bbsplit - stub": { "content": [ @@ -2227,8 +2227,8 @@ "15": [ "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ], "2": [ "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -2302,15 +2302,15 @@ "versions": [ "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:50:45.029123" + "timestamp": "2024-10-21T14:35:46.545484011" } } \ No newline at end of file diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test.snap b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap index 847be5d62..53368a78f 100644 --- a/subworkflows/local/quantify_rsem/tests/main.nf.test.snap +++ b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap @@ -60,13 +60,13 @@ "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "17": [ + "versions.yml:md5,0f2bbea6c0412d2b185eab2dd0db06d5", + "versions.yml:md5,2a8e04c552c56aacc9a2d158fbc23a89", "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", - "versions.yml:md5,3399809728955f4654ab781f37ea42d3", - "versions.yml:md5,4219f710ca21b71a7c7db6b02ac19bb3", - "versions.yml:md5,912c613bca84f899b3e890985ecc6fc2", - "versions.yml:md5,a4755dd9acbfa60dbc38e172ffda193f", + "versions.yml:md5,7696e625e0eda9d9ae30c8d5b3d23d9f", "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c", - "versions.yml:md5,f645ee5b20a4e89c6ed48fdc27c21791" + "versions.yml:md5,f151349bd7086cb08134496033e78cea", + "versions.yml:md5,ff8adbe60177b3dba23d91b3424b10b6" ], "2": [ [ @@ -258,21 +258,21 @@ ] ], "versions": [ + "versions.yml:md5,0f2bbea6c0412d2b185eab2dd0db06d5", + "versions.yml:md5,2a8e04c552c56aacc9a2d158fbc23a89", "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", - "versions.yml:md5,3399809728955f4654ab781f37ea42d3", - "versions.yml:md5,4219f710ca21b71a7c7db6b02ac19bb3", - "versions.yml:md5,912c613bca84f899b3e890985ecc6fc2", - "versions.yml:md5,a4755dd9acbfa60dbc38e172ffda193f", + "versions.yml:md5,7696e625e0eda9d9ae30c8d5b3d23d9f", "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c", - "versions.yml:md5,f645ee5b20a4e89c6ed48fdc27c21791" + "versions.yml:md5,f151349bd7086cb08134496033e78cea", + "versions.yml:md5,ff8adbe60177b3dba23d91b3424b10b6" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:32:06.579549" + "timestamp": "2024-10-21T14:49:44.270456428" }, "homo_sapiens": { "content": [ diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap index 4fd70b5f3..d39f9129b 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "test" }, - "test.stats:md5,09d1bd8f10e000921202f7ea1cd0679e" + "test.stats:md5,84891a894010aeb882c4092db9248d2c" ] ], [ @@ -26,18 +26,18 @@ ] ], [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ] ], "meta": { - 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"versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:34:35.959581" + "timestamp": "2024-09-16T08:04:43.790052381" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index 32788a18c..092a78d6d 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -5,20 +5,20 @@ "test.cram.crai:md5,78d47ba01ac4e05f3ae1e353902a989e", "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", - 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"test.stats:md5,4a0c429c661d6aa0b60acb9309da642d" + "test.stats:md5,291bb2393ec947140d12d42c2795b222" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:25.801394" + "timestamp": "2024-09-16T08:07:49.731645858" }, "test_bam_stats_samtools_paired_end": { "content": [ @@ -291,20 +291,20 @@ "id": "test", "single_end": true }, - "test.stats:md5,7afd486ad6abb9a2a3dac90c99e1d87b" + "test.stats:md5,8140d69cdedd77570ca1d7618a744e16" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - 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"nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:22:51.388076" + "timestamp": "2024-10-18T10:48:45.587883209" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test index 0048b3b33..37dd098cd 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test @@ -5,6 +5,9 @@ nextflow_workflow { workflow "FASTQ_ALIGN_HISAT2" config "./nextflow.config" + + + setup { run("HISAT2_EXTRACTSPLICESITES") { script "../../../../modules/nf-core/hisat2/extractsplicesites/main.nf" diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap index 408dabff0..f5a872982 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap @@ -34,7 +34,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,845655ccfd1fd701b9f692f8db9508af" + "test.stats:md5,0ebab7bf6149e6378b263997d7073067" ] ], [ @@ -47,19 +47,19 @@ ] ], [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:36:06.813423" + "timestamp": "2024-09-16T08:27:35.808393107" }, "sarscov2 - bam - single_end - stub": { "content": [ @@ -134,12 +134,12 @@ ] ], "9": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ], "bai": [ [ @@ -211,20 +211,20 @@ ] ], "versions": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:36:23.861012" + "timestamp": "2024-09-16T08:10:09.451605417" }, "sarscov2 - bam - paired_end": { "content": [ @@ -261,7 +261,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,603fa8c9e0e9eb3769498fc989a29250" + "test.stats:md5,74b78cbd41df459e1037735f714cda4f" ] ], [ @@ -274,19 +274,19 @@ ] ], [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:36:25.071168" + "timestamp": "2024-09-16T08:28:01.671969576" }, "sarscov2 - bam - paired_end - stub": { "content": [ @@ -361,12 +361,12 @@ ] ], "9": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ], "bai": [ [ @@ -438,19 +438,19 @@ ] ], "versions": [ - 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test("skip_umi_extract") { when { @@ -675,7 +674,6 @@ nextflow_workflow { } } - test("skip_umi_extract - stub") { options "-stub" diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test index 3fffd234b..1043d06ad 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -5,6 +5,7 @@ nextflow_workflow { workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE" config './nextflow.config' + test("test single end read with UMI") { when { diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index 46bf3acf2..834aaa931 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -60,9 +60,9 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -122,17 +122,17 @@ ] ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:34.919444" + "timestamp": "2024-10-22T19:25:19.153139356" }, "test paired end read without UMI - stub": { "content": [ @@ -192,8 +192,8 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -250,16 +250,16 @@ ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:51.765414" + "timestamp": "2024-10-22T19:25:30.433084765" }, "test paired end read without UMI": { "content": [ @@ -288,15 +288,15 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:05:37.366404" + "timestamp": "2024-10-22T19:24:40.341840093" }, "test single end read with UMI": { "content": [ @@ -322,16 +322,16 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:04:53.072227" + "timestamp": "2024-10-22T19:24:09.307037853" }, "test paired end read with UMI": { "content": [ @@ -357,16 +357,16 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:05:16.709704" + "timestamp": "2024-10-22T19:24:26.93011239" }, "test skip all steps": { "content": [ @@ -447,9 +447,9 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -509,16 +509,16 @@ ] ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:09.844235" + "timestamp": "2024-10-22T19:25:05.585472049" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap index e0c944f31..d0509e559 100644 --- a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap @@ -29,15 +29,15 @@ ] ], [ - "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c", + "versions.yml:md5,eb47b2c20a3565e58b613f66521da320" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:08:35.832206" + "timestamp": "2024-10-19T17:28:10.525956442" }, "homo_sapiens paired-end [fastq] - stub": { "content": [ @@ -103,8 +103,8 @@ ] ], "5": [ - "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c", + "versions.yml:md5,eb47b2c20a3565e58b613f66521da320" ], "index": [ [ @@ -167,15 +167,15 @@ ] ], "versions": [ - "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c", + "versions.yml:md5,eb47b2c20a3565e58b613f66521da320" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:08:56.819" + "timestamp": "2024-10-19T17:28:28.896824153" } } \ No newline at end of file diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test index d0a59629e..9c484b4aa 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_workflow { script "../main.nf" workflow "QUANTIFY_PSEUDO_ALIGNMENT" + test("salmon") { setup { diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap index 4db35cced..18a5eb761 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap @@ -54,17 +54,17 @@ ] ], [ - "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96", + "versions.yml:md5,be28c034506b52fd01f9b2fb0fc678e3", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", - "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" + "versions.yml:md5,efbc421f11a829423221fc2e67e03892" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:36:19.861809" + "timestamp": "2024-10-18T10:06:55.431718491" }, "salmon - stub": { "content": [ @@ -122,9 +122,9 @@ ] ], "14": [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ], "2": [ @@ -308,18 +308,18 @@ ] ], "versions": [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:36:55.281379" + "timestamp": "2024-10-18T10:07:30.425544183" }, "kallisto - stub": { "content": [ @@ -375,10 +375,10 @@ ] ], "14": [ - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", - "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" + "versions.yml:md5,efbc421f11a829423221fc2e67e03892" ], "2": [ [ @@ -559,18 +559,18 @@ ] ], "versions": [ - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", - "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" + "versions.yml:md5,efbc421f11a829423221fc2e67e03892" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:37:29.239014" + "timestamp": "2024-10-18T10:08:20.127524239" }, "salmon": { "content": [ @@ -629,16 +629,16 @@ ] ], [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96", + "versions.yml:md5,be28c034506b52fd01f9b2fb0fc678e3", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:35:48.954002" + "timestamp": "2024-10-18T10:06:18.517305145" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc432a..1638a410b 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "UTILS_NFSCHEMA_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/utils_nfschema_plugin" - tag "plugin/nf-schema" config "./nextflow.config" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index c9981b3d1..4165436ac 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -4,16 +4,16 @@ 22, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -31,19 +31,19 @@ "gunzip": 1.1 }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -88,31 +88,31 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T09:21:27.152841" + "timestamp": "2024-10-23T10:43:40.33664602" }, "Params: default": { "content": [ 198, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -129,7 +129,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -174,45 +174,45 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -221,13 +221,13 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1300,59 +1300,59 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", + "multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d", + "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", - "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", + "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882", + "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5", + "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1360,53 +1360,53 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00", + "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", + "WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,2a5c8c10f4371048d7d459411b58b087", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a8ad2573b09fbef181d2d5792a74dbd4", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", - "WT_REP1.biotype_counts_mqc.tsv:md5,cac41767a8cc2e5fee58637971ec89d1", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,c97046671b304b69811872854c361450", + "WT_REP1.biotype_counts_mqc.tsv:md5,3d9d1dca4551ff5689f36ba3f23848f2", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,112001ddbe917d935ee276d1685840bd", - "WT_REP2.biotype_counts_mqc.tsv:md5,e61b72317ac3c4d4ac64b663145e6262", + "WT_REP1.featureCounts.txt:md5,e64f59d719d21293627717beb76beaf5", + "WT_REP2.biotype_counts_mqc.tsv:md5,5cb8f29f175d07b3d8f8464bf8fcd82b", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,59e23ae18cfe6aa2e5a884bc03cbff15", + "WT_REP2.featureCounts.txt:md5,0f3ed14df2ca681161c63aed8e6a7c7c", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", @@ -1421,9 +1421,9 @@ "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", - "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "coverage_profile_along_genes_(high).txt:md5,3863e6277dc95e3fac3f9cd5095a08eb", + "coverage_profile_along_genes_(low).txt:md5,df84b2f592a0f02310096a2dd053397d", + "coverage_profile_along_genes_(total).txt:md5,df84b2f592a0f02310096a2dd053397d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", @@ -1445,7 +1445,7 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "e_data.ctab:md5,7cc6dedfc89b50e4be8c3ba82ba4f8aa", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", @@ -1457,8 +1457,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T09:48:14.477734" + "timestamp": "2024-10-23T10:42:45.202573855" } -} +} \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index b14b204a7..dfd3f3d2c 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -4,16 +4,16 @@ 22, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -31,19 +31,19 @@ "gunzip": 1.1 }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -88,31 +88,31 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:00:44.36432" + "timestamp": "2024-10-23T10:54:29.62339584" }, "Params: --featurecounts_group_type false": { "content": [ 188, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -129,7 +129,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -171,42 +171,42 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -215,13 +215,13 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1266,58 +1266,58 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", + "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", - "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", + "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882", + "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5", + "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1325,37 +1325,37 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00", + "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", + "WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", @@ -1371,9 +1371,9 @@ "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", - "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "coverage_profile_along_genes_(high).txt:md5,3863e6277dc95e3fac3f9cd5095a08eb", + "coverage_profile_along_genes_(low).txt:md5,df84b2f592a0f02310096a2dd053397d", + "coverage_profile_along_genes_(total).txt:md5,df84b2f592a0f02310096a2dd053397d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", @@ -1395,7 +1395,7 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "e_data.ctab:md5,7cc6dedfc89b50e4be8c3ba82ba4f8aa", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", @@ -1407,8 +1407,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:00:00.235948" + "timestamp": "2024-10-23T10:53:28.969150716" } -} +} \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index dd6b9d23e..4b39b7703 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -4,16 +4,16 @@ 23, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -34,8 +34,8 @@ "hisat2": "2.2.1" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_HISAT2_INDEX": { "untar": 1.34 @@ -44,7 +44,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -89,31 +89,31 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:10:47.69497" + "timestamp": "2024-10-23T11:01:31.33505759" }, "Params: --aligner hisat2": { "content": [ 187, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -126,7 +126,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -178,35 +178,35 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -215,7 +215,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_HISAT2_INDEX": { "untar": 1.34 @@ -224,7 +224,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1177,21 +1177,21 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,117712525fcbd396f77710f4f4b605d9", "WT_REP1_intercept_slope.txt:md5,df33cbc6c3cb1c85c0c06cdba7df3873", "WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,079b099e5c5e9fe5e2559dfc938aa48b", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,cd7494b3bb12295a287f36506638f3c6", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,eedff929765dbc950528ee499e6d63ba", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,a60088d7013eebeb240e02457431eedb", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,4d1820a35481f454f17a14326356253d", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,b007abbc78b08d8d2bb37a267665947d", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,3e6a34d7435d5249229c849532a45930", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,3632da2126cb33391428ba0d6d10787f", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,ea897231d1c447d8e395716741b876ab", - "WT_REP1.biotype_counts_mqc.tsv:md5,abc303e93390bb5bd8f916f8f5978de3", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,72513319be04c591dcbbaf14f2081b32", + "WT_REP1.biotype_counts_mqc.tsv:md5,4b2f1b065666fbe235aa72ba06142025", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,39721c0d981304996438bc2f505bf98c", - "WT_REP2.biotype_counts_mqc.tsv:md5,74a5436a716a7d99f425f73914cb2794", + "WT_REP1.featureCounts.txt:md5,8faf3b2101c5e07bbf02415663855690", + "WT_REP2.biotype_counts_mqc.tsv:md5,994f8e87aeaa769479fcc4747ffbe6d9", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,702446d50a5019c84fcef85d1cfef78c", + "WT_REP2.featureCounts.txt:md5,efa5c0e711a3e0bdd42035be239e04a2", "coverage_profile_along_genes_(high).txt:md5,b56043c3546cac003461c57abad93536", "coverage_profile_along_genes_(low).txt:md5,1b55d86defcc541643137497c4c6bb06", "coverage_profile_along_genes_(total).txt:md5,1b55d86defcc541643137497c4c6bb06", @@ -1247,19 +1247,19 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", + "multiqc_featurecounts_biotype_plot.txt:md5,d784fc4b2dce860c8f88cc3e936e589e", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1275,31 +1275,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" @@ -1307,8 +1307,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T12:37:31.888584" + "timestamp": "2024-10-23T11:00:43.422573373" } -} +} \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 4cc4ac925..8bd57f925 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -4,22 +4,22 @@ 35, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -34,20 +34,20 @@ "gunzip": 1.1 }, "KALLISTO_INDEX": { - "kallisto": "0.48.0" + "kallisto": "0.51.1" }, "KALLISTO_QUANT": { - "kallisto": "0.48.0" + "kallisto": "0.51.1" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -56,7 +56,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -236,40 +236,40 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233" + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-09T19:19:07.816437" + "timestamp": "2024-10-23T11:04:57.579312846" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ 17, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "GTF2BED": { "perl": "5.26.2" @@ -284,17 +284,17 @@ "gunzip": 1.1 }, "KALLISTO_INDEX": { - "kallisto": "0.48.0" + "kallisto": "0.51.1" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -327,8 +327,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-09T18:56:35.320816" + "timestamp": "2024-10-23T11:05:54.052864085" } -} +} \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 2799bc339..bc6454c98 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -4,22 +4,22 @@ 152, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -36,7 +36,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -81,45 +81,45 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -128,13 +128,13 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1041,21 +1041,21 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", + "multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476", + "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1065,36 +1065,36 @@ "rseqc_infer_experiment_plot.txt:md5,749a802379ada3ec9d2083ecbe6aef7e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1102,27 +1102,27 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", @@ -1130,15 +1130,15 @@ "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,2a5c8c10f4371048d7d459411b58b087", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a8ad2573b09fbef181d2d5792a74dbd4", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,c97046671b304b69811872854c361450", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", @@ -1173,25 +1173,25 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:36:48.24104" + "timestamp": "2024-10-23T11:18:04.553985917" }, "Params: --min_mapped_reads 90 - stub": { "content": [ 22, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -1209,19 +1209,19 @@ "gunzip": 1.1 }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1266,8 +1266,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:37:37.274627" + "timestamp": "2024-10-23T11:19:22.443482528" } -} +} \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 4b477e6a7..0a379aea9 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -4,22 +4,22 @@ 205, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -36,7 +36,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -81,51 +81,51 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "SORTMERNA": { - "sortmerna": "4.3.6" + "sortmerna": "4.3.7" }, "SORTMERNA_INDEX": { - "sortmerna": "4.3.6" + "sortmerna": "4.3.7" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -134,13 +134,13 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1227,59 +1227,59 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", - "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", + "multiqc_featurecounts_biotype_plot.txt:md5,f4de303d3277d862031df94b509527ba", + "multiqc_samtools_idxstats.txt:md5,58f19b28617037a2825f812d58d55e2e", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Counts.txt:md5,50e9209baeaafe181ce3b5caa05cf789", - "qualimap_gene_coverage_profile_Normalised.txt:md5,6ed32f112c679e73396350cbe5cb9459", - "qualimap_rnaseq_cov_hist.txt:md5,a895b3af229f661da1edbc21ec72edaa", + "qualimap_gene_coverage_profile_Counts.txt:md5,286d47f67e1d034a88e122091ae30f3d", + "qualimap_gene_coverage_profile_Normalised.txt:md5,3297068282f57506f40070b8bc6ad1b5", + "qualimap_rnaseq_cov_hist.txt:md5,a523cfcb52fe8f2d5902d933568a790d", "rseqc_infer_experiment_plot.txt:md5,d8741451248f1a5a4ebe3230c1af9c95", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,4ff26c0457ddceb4a03e874222b46f00", "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,306609f606004616a89ec50dc59f22b0", + "cmd_info.json:md5,3fa4eede50b6057d7ea52ca8aff1d641", "lib_format_counts.json:md5,b814fed52bd197a64544086dba0f127a", "ambig_info.tsv:md5,c83b0f9ebe9b8dfc284595ec56d4f092", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,6b367a9cdd2837b88890209459acf45f", + "cmd_info.json:md5,c5c31cc1202236ae2c800526c8a72827", "lib_format_counts.json:md5,3f4d67ace359562564dd336aa47a479c", "ambig_info.tsv:md5,00a1f9de7095a68dfb43e0a0301b6ecd", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c8c6208e1082ec150de56679b2b8cfe3", + "cmd_info.json:md5,e20c14f481b4468e11664f04ac06b166", "lib_format_counts.json:md5,f56087bcbd494c7fa78200f65a2400e2", "ambig_info.tsv:md5,54d942ddf69b4e8f1598064e09428256", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,5523405c02d30489d276e5d734cb54da", + "cmd_info.json:md5,8e239ec68573adbfcbcbac9238a1d433", "lib_format_counts.json:md5,43fc5463eada79e466d6ba9848739f06", "ambig_info.tsv:md5,933feffdaf6cf6ff407469ade0d7684d", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,998c89efb00fa5e63fd1d18c0602a019", + "cmd_info.json:md5,fa7b659f1ba90e16b0d0a375ff318b01", "lib_format_counts.json:md5,e6e3d7746e9abee6a0e097ae0ee1781a", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1287,53 +1287,53 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8611b6c03f6aa1a5f3dfceb0e65ad4ef", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,1b69f9b651dfa6799e310004c1e3309f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,070c7d50eab5ce0f211cdb06f9d7cc29", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,b8c61854b56a1c9a0fc8f158ea0c7599", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc", - "WT_REP1_dupMatrix.txt:md5,b0de1683f2a9bfa42437e924a11648fd", + "WT_REP1_dupMatrix.txt:md5,b82c4fed335d03e85c414c91c2efd461", "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217", - "WT_REP1_intercept_slope.txt:md5,f38c8525b7fcb990b7158f1518e451ad", + "WT_REP1_intercept_slope.txt:md5,7db7a898152e8eaab96b1aaf0e567e50", "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f36792d25b268b6d556f8728300f4afc", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,accedae963f399d3b47effd8eda41edb", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,c5865ded7168476d93057d2aedaec694", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,e37ededa12690a8ccae2eb42dac47ed6", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,782f5001d411ba79314ba77f7d36b157", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a0fb30c2b937a5a41ac865ab09367af7", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,84cdcb79270d27007457fcaed5a1ad1b", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,1c9d07d9f9d12219d2b9f761f854eced", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,de016e691f5d56b13bbaa626ce2cc93e", - "WT_REP1.biotype_counts_mqc.tsv:md5,eca4a76b9243248d01df5f4289b8201e", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,109c8988ccc98e6d2a45c3d55b07f2bd", + "WT_REP1.biotype_counts_mqc.tsv:md5,97caee79e83b5fce6e5504c0daefe474", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,7aadafd0a26f5047a9ae7266eccfce05", - "WT_REP2.biotype_counts_mqc.tsv:md5,530605b80da27915a90d452249f3243a", + "WT_REP1.featureCounts.txt:md5,2d37cf435f77164dc9dfd11725b60528", + "WT_REP2.biotype_counts_mqc.tsv:md5,e6bec82076f4cb2eff39f0d1bae70dc9", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,809af01851125c401d576c21efca7b5a", + "WT_REP2.featureCounts.txt:md5,dd94f2f0c2ca58b9436429e33effd524", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", @@ -1348,9 +1348,9 @@ "coverage_profile_along_genes_(high).txt:md5,634f447f91db940d2148af74cf36febd", "coverage_profile_along_genes_(low).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", "coverage_profile_along_genes_(total).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", - "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb", - "coverage_profile_along_genes_(low).txt:md5,b2c696661e6c524b1641eb7267c70edc", - "coverage_profile_along_genes_(total).txt:md5,b2c696661e6c524b1641eb7267c70edc", + "coverage_profile_along_genes_(high).txt:md5,40b488dc478b4bf6d802319e89846c0a", + "coverage_profile_along_genes_(low).txt:md5,9f1e68e98d4d663aac436305c99cceaf", + "coverage_profile_along_genes_(total).txt:md5,9f1e68e98d4d663aac436305c99cceaf", "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294", "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd", "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd", @@ -1372,7 +1372,7 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,682817a9d0a1ac9c1637249e007d3514", + "e_data.ctab:md5,68812b283993f721b237ae6cdecc30d5", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", @@ -1384,25 +1384,25 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:03:32.596507" + "timestamp": "2024-10-23T11:36:09.902195192" }, "Params: --remove_ribo_rna - stub": { "content": [ 24, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -1420,22 +1420,22 @@ "gunzip": 1.1 }, "SORTMERNA_INDEX": { - "sortmerna": "4.3.6" + "sortmerna": "4.3.7" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1480,8 +1480,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:04:25.816703" + "timestamp": "2024-10-23T11:37:11.90905171" } -} +} \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 0293e72fa..1e6827546 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -4,22 +4,22 @@ 34, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -34,14 +34,14 @@ "gunzip": 1.1 }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -50,7 +50,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -281,71 +281,71 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T07:25:22.063836" + "timestamp": "2024-10-23T11:41:47.859384178" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ 16, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "GTF2BED": { "perl": "5.26.2" @@ -360,14 +360,14 @@ "gunzip": 1.1 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -400,8 +400,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T07:07:48.845197" + "timestamp": "2024-10-23T11:42:36.34114827" } -} +} \ No newline at end of file diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 70b17efcb..a07a6dd43 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -4,16 +4,16 @@ 17, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "GTF2BED": { "perl": "5.26.2" @@ -28,19 +28,19 @@ "gunzip": 1.1 }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -74,34 +74,34 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:17:30.991115" + "timestamp": "2024-10-23T11:50:42.323505833" }, "Params: --skip_qc": { "content": [ 136, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -119,42 +119,42 @@ "picard": "3.1.1" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -163,13 +163,13 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -681,80 +681,80 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", + "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", @@ -773,7 +773,7 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "e_data.ctab:md5,7cc6dedfc89b50e4be8c3ba82ba4f8aa", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", @@ -785,8 +785,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:16:41.081492" + "timestamp": "2024-10-23T11:49:49.131172185" } -} +} \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index bfc0873a4..a0bfa97e4 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -4,22 +4,22 @@ 193, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -36,7 +36,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -81,41 +81,41 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -124,13 +124,13 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1110,7 +1110,7 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_featurecounts_biotype_plot.txt:md5,567475905baa63091cfd0560fb297e10", + "multiqc_featurecounts_biotype_plot.txt:md5,91d4ea5a6d4b02091be666eeab952443", "multiqc_samtools_idxstats.txt:md5,adf5f32fa1485ad0f4dacdfedc7b4bbc", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1126,31 +1126,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,406e1457f0f0506bd8e605a217477436", "ambig_info.tsv:md5,0e0895adb376929bec8e0dd0677bf7d8", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,afd2a0ddf0fd0ec4f99be898608a59db", "ambig_info.tsv:md5,6ed1b46c69917d6af3f093f9503bb962", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,f7b7048fd2ac63fd792e71b85e4ed6d1", "ambig_info.tsv:md5,2f4c6a5953e41252a89851a9a7c36d9b", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,03f0b70a4bb428fab96c29f04f895b6f", "ambig_info.tsv:md5,5fff63493bf3c223707ac90b9bb3a8f3", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,4bf135c93c37f90c493f761f2709a28b", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1158,27 +1158,27 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,452bbc83465339d2467663b061400b95", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,f2aed38ba5251664024392bc89ae3f01", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,8d2b5ec0c441d9e078610480d179d116", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,44dad5d05b3c0c2ccb5a19a3a80333b3", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,fdeebc4f056cbb52fee53e82c2e0096f", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,aa94a148bdbebec4e82cd18a00316506", @@ -1190,21 +1190,21 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,147b051de3f1e5c75821176851d13612", "WT_REP1_intercept_slope.txt:md5,395cde13da1a90cf4378be2597c4f297", "WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,27087a1c2e3cc2a0826818a04fe2647f", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,bc80cee5887507179965623c3dfef4f9", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,e8ec41e6e79f378e2f301e245a4f8e73", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b1ed22e51a94a0ca8f030ff4e09295aa", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,2e1d531352e9ad5935308e588dbaffe7", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,3afe2b0bcf265526c247016c32482314", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a0ba869a8538e9bff9bf5976cdeecda6", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,6fedc1d11bc8d558f61c4c4a6060040f", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,6fed16d5ab57aa762891fde0c3720160", - "WT_REP1.biotype_counts_mqc.tsv:md5,ddcf909eacd91a49cc4fd3beed0b74f4", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,392538c1d377a72f6d89e5ace7e69bcd", + "WT_REP1.biotype_counts_mqc.tsv:md5,159e8125673fd75086d352ca1359d7b7", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,5155de67cf7537016c9ded607797f5c5", - "WT_REP2.biotype_counts_mqc.tsv:md5,d5d731cea7c5083a54069c1820101ba3", + "WT_REP1.featureCounts.txt:md5,f244c5de5ffa4afdf4d23becf4fa8c8d", + "WT_REP2.biotype_counts_mqc.tsv:md5,70bdca053da2f6f8a1aa29a5e32d2228", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,94d2ccd74ec4338ddc8ad7bdbf297826", + "WT_REP2.featureCounts.txt:md5,24b7f969ede9c698de30aa0b3f881b8b", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,20c790387ef68e041bc4ffdcd032a22f", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,ba2636236fa1d26aa72f7aff73bd41f8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1c0458f66e4af56a56f4409c120434b3", @@ -1255,8 +1255,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:28:37.351353" + "timestamp": "2024-10-21T20:23:07.88998048" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index d46ed0819..31e9150d8 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -4,22 +4,22 @@ 188, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -36,7 +36,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -88,35 +88,35 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -125,7 +125,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_RSEM_INDEX": { "untar": 1.34 @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1138,19 +1138,19 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", + "multiqc_featurecounts_biotype_plot.txt:md5,aef45c9c7814f3127cd3e9b77a5ed676", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1166,31 +1166,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1205,21 +1205,21 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,a1c5346e3bad40546c793b8914a22e7e", "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965", "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,e66cd2b584d970ae3827ad2521f795ca", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,5a7a4291e8ff6cc25a4eb72dfdf06b51", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b3013c797d2fd38a8efa39047f5ba1b1", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,a8200ec76e7916dc1210447130f77bbf", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,548023e639f8eb76f973a2f98bcbc82c", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,ff59317794fc04d5a4fd18797f0ecb0f", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,577cd26ea14a25d5f667f05ef6d62816", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,2c0b5696582493f7a50259679982a6b3", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,6ee84531ba255791a11b487b6aea75ab", - "WT_REP1.biotype_counts_mqc.tsv:md5,512645a8f736eee160c4465e1940f4a5", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,e405c75b21f6e8113ca8e114e9ae1f20", + "WT_REP1.biotype_counts_mqc.tsv:md5,d083ca421266ae2d4b3cd745b41ae110", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,289cc95971a3ec550e018659279c1f59", - "WT_REP2.biotype_counts_mqc.tsv:md5,d4957c0197636b68d27fbd60d388bba1", + "WT_REP1.featureCounts.txt:md5,32185355effd40ec8cdc1ee41dfd48ef", + "WT_REP2.biotype_counts_mqc.tsv:md5,c04c2936bbfac3bff284f96b7233b158", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,152d2f26df56a88fe4b27c742d8f7447", + "WT_REP2.featureCounts.txt:md5,04c506ad79af5295666847fa729e691c", "coverage_profile_along_genes_(high).txt:md5,31ab137e75752225365bd3d89143dbd2", "coverage_profile_along_genes_(low).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", "coverage_profile_along_genes_(total).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", @@ -1268,25 +1268,25 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T12:45:00.993602" + "timestamp": "2024-10-23T12:16:02.205058346" }, "Params: --aligner star_rsem - stub": { "content": [ 22, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -1304,8 +1304,8 @@ "gunzip": 1.1 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.9 }, "UNTAR_RSEM_INDEX": { "untar": 1.34 @@ -1314,7 +1314,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1359,8 +1359,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:41:09.240442" + "timestamp": "2024-10-23T12:17:33.292700445" } -} +} \ No newline at end of file diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 260cc8c1d..08360f58c 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: # Important checks and failures sample-status: