From 2efe5e45d4eb69fc0090d4ec99bac58a19fc5c22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Thu, 9 Jan 2025 10:21:02 +0100 Subject: [PATCH] revert changes that do not belong to template update --- bin/vcf2counts.R | 43 + conf/test.config | 10 +- conf/test_full.config | 8 +- docs/output.md | 4 +- docs/usage.md | 12 +- main.nf | 14 +- modules.json | 5 + modules/local/vcf2mat/environment.yml | 7 + modules/local/vcf2mat/main.nf | 45 + .../nf-core/bcftools/merge/environment.yml | 5 + modules/nf-core/bcftools/merge/main.nf | 74 ++ modules/nf-core/bcftools/merge/meta.yml | 96 ++ .../nf-core/bcftools/merge/tests/bcf.config | 3 + .../bcftools/merge/tests/bcf_gz.config | 3 + .../nf-core/bcftools/merge/tests/main.nf.test | 853 ++++++++++++++++++ .../bcftools/merge/tests/main.nf.test.snap | 607 +++++++++++++ .../bcftools/merge/tests/nextflow.config | 5 + .../bcftools/merge/tests/nextflow.gvcf.config | 5 + modules/nf-core/bcftools/merge/tests/tags.yml | 2 + .../nf-core/bcftools/merge/tests/vcf.config | 3 + .../bcftools/merge/tests/vcf_gz.config | 3 + .../bcftools/merge/tests/vcf_gz_index.config | 3 + .../merge/tests/vcf_gz_index_csi.config | 3 + .../merge/tests/vcf_gz_index_tbi.config | 3 + .../gatk4/genotypegvcfs/environment.yml | 10 + modules/nf-core/gatk4/genotypegvcfs/main.nf | 68 ++ modules/nf-core/gatk4/genotypegvcfs/meta.yml | 117 +++ .../gatk4/genotypegvcfs/tests/main.nf.test | 285 ++++++ .../genotypegvcfs/tests/main.nf.test.snap | 191 ++++ modules/nf-core/tabix/tabix/environment.yml | 7 + modules/nf-core/tabix/tabix/main.nf | 45 + modules/nf-core/tabix/tabix/meta.yml | 58 ++ .../nf-core/tabix/tabix/tests/main.nf.test | 136 +++ .../tabix/tabix/tests/main.nf.test.snap | 212 +++++ .../tabix/tabix/tests/tabix_bed.config | 5 + .../tabix/tabix/tests/tabix_gff.config | 5 + .../tabix/tabix/tests/tabix_vcf_csi.config | 5 + .../tabix/tabix/tests/tabix_vcf_tbi.config | 5 + modules/nf-core/tabix/tabix/tests/tags.yml | 2 + .../utils_nfcore_vcftomat_pipeline/main.nf | 18 +- tests/nextflow.config | 36 + workflows/vcftomat.nf | 6 +- 42 files changed, 2993 insertions(+), 34 deletions(-) create mode 100755 bin/vcf2counts.R create mode 100644 modules/local/vcf2mat/environment.yml create mode 100644 modules/local/vcf2mat/main.nf create mode 100644 modules/nf-core/bcftools/merge/environment.yml create mode 100644 modules/nf-core/bcftools/merge/main.nf create mode 100644 modules/nf-core/bcftools/merge/meta.yml create mode 100644 modules/nf-core/bcftools/merge/tests/bcf.config create mode 100644 modules/nf-core/bcftools/merge/tests/bcf_gz.config create mode 100644 modules/nf-core/bcftools/merge/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/merge/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/merge/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config create mode 100644 modules/nf-core/bcftools/merge/tests/tags.yml create mode 100644 modules/nf-core/bcftools/merge/tests/vcf.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/gatk4/genotypegvcfs/environment.yml create mode 100644 modules/nf-core/gatk4/genotypegvcfs/main.nf create mode 100644 modules/nf-core/gatk4/genotypegvcfs/meta.yml create mode 100644 modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/tabix/environment.yml create mode 100644 modules/nf-core/tabix/tabix/main.nf create mode 100644 modules/nf-core/tabix/tabix/meta.yml create mode 100644 modules/nf-core/tabix/tabix/tests/main.nf.test create mode 100644 modules/nf-core/tabix/tabix/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_bed.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_gff.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config create mode 100644 modules/nf-core/tabix/tabix/tests/tags.yml create mode 100644 tests/nextflow.config diff --git a/bin/vcf2counts.R b/bin/vcf2counts.R new file mode 100755 index 0000000..9c8bdba --- /dev/null +++ b/bin/vcf2counts.R @@ -0,0 +1,43 @@ +#!/usr/bin/env Rscript +'VCF to count matrix converter + +Usage: + vcf2counts.R --help + vcf2counts.R --output= VCF + +Options: + -h, --help help screen + -o, --output= output file name [default: mat.csv] + +Arguments: + VCF input vcf file +'->doc + +suppressMessages(library(VariantAnnotation, warn.conflicts = FALSE, quietly=TRUE)) +suppressMessages(library(docopt, warn.conflicts = FALSE, quietly=TRUE)) +suppressMessages(library(Matrix, warn.conflicts = FALSE, quietly=TRUE)) + +generateMatrixfromVCF <- function(VCF, ofile) { + # Read in VCF file + vcfobj <- readVcf(VCF) + # Convert genotype to SNP matrix + genomat <- geno(vcfobj)$GT + + variantmat <- apply(genomat, c(1, 2), function(x) { + xstrip <- gsub("[[:punct:]]", "", x) + if (xstrip == "11") { + return (2) + } else if (xstrip %in% c("01", "10")) { + return (1) + } else if (xstrip %in% c("00", "")) { + return (0) + } else { + return (NA) + } + }) + write.csv(variantmat, file = ofile) +} + +opt <- docopt(doc) + +generateMatrixfromVCF(opt$VCF, opt[["--output"]]) diff --git a/conf/test.config b/conf/test.config index 79b4bcc..53c7fda 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,13 +20,7 @@ process { params { config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset to check pipeline function' + config_profile_description = 'Minimal test dataset to check pipeline function. Skips processes GATK_GENOTYPEGVCFS and BCFTOOLS_MERGE.' - // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - - // Genome references - genome = 'R64-1-1' + input = "${projectDir}/tests/input.csv" } diff --git a/conf/test_full.config b/conf/test_full.config index 2b02e06..df19465 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,10 +15,10 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + input = "${projectDir}/tests/input-full.csv" // Genome references - genome = 'R64-1-1' + fasta = "https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta" + fai = "https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai" + dict = "https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.dict" } diff --git a/docs/output.md b/docs/output.md index f8d3603..82c23e5 100644 --- a/docs/output.md +++ b/docs/output.md @@ -57,7 +57,9 @@ A custom R script is used to convert the finalized VCF to a CSV which can be use [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see .### Pipeline information +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . + +### Pipeline information
Output files diff --git a/docs/usage.md b/docs/usage.md index ee708c1..9d8cefa 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -4,19 +4,19 @@ ## Introduction - +This document describes the usage of the pipeline. The pipeline processes (g)VCF files coming from different variant calling pipelines and converts them to a matrix format which is suitable for downstream clustering analysis. The pipeline is built using [Nextflow](https://www.nextflow.io/). ## Samplesheet input -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. +You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below. ```bash ---input '[path to samplesheet file]' +--input '[path to samplesheet file]' --genome '[genome version]' ``` -### Multiple runs of the same sample +### Same sample, different callers -The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: +The `sample` identifiers have to be the same when the vcfs originate from the same bam but were yielded with different callers. The pipeline will merge all vcfs from the same sample into one vcf file but is also able to handle if there is only one vcf file for a sample (merging will then be skipped). ```csv title="samplesheet.csv" sample,label,gvcf,vcf_path,vcf_index_path @@ -113,7 +113,7 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli > [!IMPORTANT] > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. diff --git a/main.nf b/main.nf index c9769d6..e77045c 100644 --- a/main.nf +++ b/main.nf @@ -24,10 +24,11 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_vcft ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// TODO nf-core: Remove this line if you don't need a FASTA file // This is an example of how to use getGenomeAttribute() to fetch parameters // from igenomes.config using `--genome` params.fasta = getGenomeAttribute('fasta') +params.fai = getGenomeAttribute('fasta_fai') +params.dict = getGenomeAttribute('dict') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -45,11 +46,20 @@ workflow QBICPIPELINES_VCFTOMAT { main: + // FASTA + fasta = params.fasta ? Channel.fromPath(params.fasta).collect() : Channel.value([]) + fai = params.fai ? Channel.fromPath(params.fai).collect() : Channel.value([]) + dict = params.dict ? Channel.fromPath(params.dict).collect() : Channel.value([]) + + // // WORKFLOW: Run pipeline // VCFTOMAT ( - samplesheet + samplesheet, + fasta, + fai, + dict ) emit: multiqc_report = VCFTOMAT.out.multiqc_report // channel: /path/to/multiqc_report.html diff --git a/modules.json b/modules.json index e8f8c25..ef0f8d3 100644 --- a/modules.json +++ b/modules.json @@ -29,6 +29,11 @@ "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] + }, + "tabix/tabix": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] } } }, diff --git a/modules/local/vcf2mat/environment.yml b/modules/local/vcf2mat/environment.yml new file mode 100644 index 0000000..8b3da53 --- /dev/null +++ b/modules/local/vcf2mat/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bioconductor-variantannotation + - conda-forge::r-docopt + - conda-forge::r-matrix diff --git a/modules/local/vcf2mat/main.nf b/modules/local/vcf2mat/main.nf new file mode 100644 index 0000000..264402f --- /dev/null +++ b/modules/local/vcf2mat/main.nf @@ -0,0 +1,45 @@ +process VCF2MAT { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6c/6c2dd8fc4240adf343ad71f9c56158d87f28b2577f2a6e114b7ab8406f0c4672/data' : + 'community.wave.seqera.io/library/bioconductor-variantannotation_r-docopt_r-matrix:3cf2f20fdc477746' }" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("*.csv") , emit: csv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.0.0' + """ + vcf2counts.R \\ + --output ${prefix}.csv \\ + $vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + vcf2counts.R: $VERSION + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.0.0' + """ + touch ${prefix}.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + vcf2counts.R: $VERSION + END_VERSIONS + """ +} diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml new file mode 100644 index 0000000..5c00b11 --- /dev/null +++ b/modules/nf-core/bcftools/merge/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf new file mode 100644 index 0000000..facb14e --- /dev/null +++ b/modules/nf-core/bcftools/merge/main.nf @@ -0,0 +1,74 @@ +process BCFTOOLS_MERGE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" + + input: + tuple val(meta), path(vcfs), path(tbis) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(bed) + + output: + tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf + tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs + def regions = bed ? "--regions-file $bed" : "" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + + """ + bcftools merge \\ + $args \\ + $regions \\ + --threads $task.cpus \\ + --output ${prefix}.${extension} \\ + $input + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + + """ + ${create_cmd} ${prefix}.${extension} + ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml new file mode 100644 index 0000000..2cf09a1 --- /dev/null +++ b/modules/nf-core/bcftools/merge/meta.yml @@ -0,0 +1,96 @@ +name: bcftools_merge +description: Merge VCF files +keywords: + - variant calling + - merge + - VCF +tools: + - merge: + description: | + Merge VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] + identifier: biotools:bcftools +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: file + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbis: + type: file + description: | + List containing the tbi index files corresponding to the vcfs input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: "(Optional) The fasta reference file (only necessary for the `--gvcf + FILE` parameter)" + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: "(Optional) The fasta reference file index (only necessary for + the `--gvcf FILE` parameter)" + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'genome' ] + - bed: + type: file + description: "(Optional) The bed regions to merge on" + pattern: "*.bed" +output: + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bcf,vcf}{,.gz}": + type: file + description: merged output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: index of merged output + pattern: "*.{csi,tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@nvnieuwk" + - "@ramprasadn" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@nvnieuwk" + - "@ramprasadn" diff --git a/modules/nf-core/bcftools/merge/tests/bcf.config b/modules/nf-core/bcftools/merge/tests/bcf.config new file mode 100644 index 0000000..4467d07 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/bcf.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type u --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/bcf_gz.config b/modules/nf-core/bcftools/merge/tests/bcf_gz.config new file mode 100644 index 0000000..280de8d --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/bcf_gz.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type b --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test b/modules/nf-core/bcftools/merge/tests/main.nf.test new file mode 100644 index 0000000..3995fc1 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test @@ -0,0 +1,853 @@ +nextflow_process { + + name "Test Process BCFTOOLS_MERGE" + script "../main.nf" + process "BCFTOOLS_MERGE" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/merge" + + test("sarscov2 - [vcf, tbi], [], [], []") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf output") { + + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output") { + + config "./vcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf output") { + + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf") }, + { assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output") { + + config "./bcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf.gz") }, + { assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index") { + + config "./vcf_gz_index_csi.config" + + when { + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("tbi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], bed") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output") { + + config "./nextflow.gvcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ] + input[2] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + ] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - one sample") { + + config "./nextflow.config" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub") { + + options "-stub" + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - stub") { + + options "-stub" + config "./vcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub") { + + options "-stub" + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output - stub") { + + options "-stub" + config "./bcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index - stub") { + + options "-stub" + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub") { + + options "-stub" + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index - stub") { + + options "-stub" + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("tbi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], bed - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub") { + + options "-stub" + config "./nextflow.gvcf.config" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ] + input[2] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + ] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - one sample - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap new file mode 100644 index 0000000..b3b6255 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap @@ -0,0 +1,607 @@ +{ + "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index": { + "content": [ + "e0de448dc8e712956a03ce68d79a0b3a", + "test.vcf.gz.tbi", + [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-05T12:34:16.977726522" + }, + "sarscov2 - 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[vcf, tbi], [], [], [] - bcf.gz output": { + "content": [ + "test.bcf.gz", + [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-05T11:56:56.416361069" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.config b/modules/nf-core/bcftools/merge/tests/nextflow.config new file mode 100644 index 0000000..c3f0b71 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BCFTOOLS_MERGE { + ext.args = '--force-samples --force-single --no-version' + } +} diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config b/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config new file mode 100644 index 0000000..8c457b7 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config @@ -0,0 +1,5 @@ +process { + withName: BCFTOOLS_MERGE { + ext.args = { "--force-samples --no-version --output-type z --gvcf $fasta" } + } +} diff --git a/modules/nf-core/bcftools/merge/tests/tags.yml b/modules/nf-core/bcftools/merge/tests/tags.yml new file mode 100644 index 0000000..1464d0c --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/merge: + - "modules/nf-core/bcftools/merge/**" diff --git a/modules/nf-core/bcftools/merge/tests/vcf.config b/modules/nf-core/bcftools/merge/tests/vcf.config new file mode 100644 index 0000000..759222e --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type v --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz.config b/modules/nf-core/bcftools/merge/tests/vcf_gz.config new file mode 100644 index 0000000..8b6ad8b --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type z --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config new file mode 100644 index 0000000..9f1e9b1 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config new file mode 100644 index 0000000..8308ee1 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config new file mode 100644 index 0000000..9be4075 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml new file mode 100644 index 0000000..1f7d082 --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf new file mode 100644 index 0000000..dc2813a --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -0,0 +1,68 @@ +process GATK4_GENOTYPEGVCFS { + tag "$meta.id" + 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/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" + + input: + tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(dbsnp) + tuple val(meta6), path(dbsnp_tbi) + + output: + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def input_command = input.name.endsWith(".vcf") || input.name.endsWith(".vcf.gz") ? "$input" : "gendb://$input" + def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : "" + def interval_command = intervals ? "--intervals $intervals" : "" + + def avail_mem = 3072 + if (!task.memory) { + log.info '[GATK GenotypeGVCFs] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + """ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + GenotypeGVCFs \\ + --variant $input_command \\ + --output ${prefix}.vcf.gz \\ + --reference $fasta \\ + $interval_command \\ + $dbsnp_command \\ + --tmp-dir . \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo | gzip > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml new file mode 100644 index 0000000..0c1fe49 --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/meta.yml @@ -0,0 +1,117 @@ +name: gatk4_genotypegvcfs +description: | + Perform joint genotyping on one or more samples pre-called with HaplotypeCaller. +keywords: + - gatk4 + - genotype + - gvcf + - joint genotyping +tools: + - gatk4: + description: Genome Analysis Toolkit (GATK4) + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + tool_dev_url: https://github.com/broadinstitute/gatk + doi: "10.1158/1538-7445.AM2017-3590" + licence: ["BSD-3-clause"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + gVCF(.gz) file or a GenomicsDB + pattern: "*.{vcf,vcf.gz}" + - gvcf_index: + type: file + description: | + index of gvcf file, or empty when providing GenomicsDB + pattern: "*.{idx,tbi}" + - intervals: + type: file + description: Interval file with the genomic regions included in the library + (optional) + - intervals_index: + type: file + description: Interval index file (optional) + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing fai information + e.g. [ id:'test' ] + - fai: + type: file + description: Reference fasta index file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing dict information + e.g. [ id:'test' ] + - dict: + type: file + description: Reference fasta sequence dict file + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test' ] + - dbsnp: + type: file + description: dbSNP VCF file + pattern: "*.vcf.gz" + - - meta6: + type: map + description: | + Groovy Map containing dbsnp tbi information + e.g. [ id:'test' ] + - dbsnp_tbi: + type: file + description: dbSNP VCF index file + pattern: "*.tbi" +output: + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Genotyped VCF file + pattern: "*.vcf.gz" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Tbi index for VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@santiagorevale" + - "@maxulysse" +maintainers: + - "@santiagorevale" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test new file mode 100644 index 0000000..25bc2d3 --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test @@ -0,0 +1,285 @@ +nextflow_process { + + name "Test Process GATK4_GENOTYPEGVCFS" + script "../main.nf" + process "GATK4_GENOTYPEGVCFS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/genotypegvcfs" + tag "untar" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [ + [id:"dbsnp"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists:true) + ] + input[5] = [ + [id:"dbsnp"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists:true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = UNTAR.out.untar.map { meta, gendb -> [ meta, gendb, [], [], []] } + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = UNTAR.out.untar.map { meta, gendb -> + [ + meta, + gendb, + [], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + [] + ] + } + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap new file mode 100644 index 0000000..30e2dc1 --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap @@ -0,0 +1,191 @@ +{ + "homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T11:16:45.625453031" + }, + "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T11:15:55.296562046" + }, + "homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T11:16:30.471742609" + }, + "homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "9b7d476515e07e5486633c42abd86cc" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T11:16:13.266019505" + }, + "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T11:17:19.342242664" + }, + "homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,fb1ca56ba52eb3fcda70dbef401f06b9" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T11:17:01.475664058" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml new file mode 100644 index 0000000..017c259 --- /dev/null +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf new file mode 100644 index 0000000..13acd67 --- /dev/null +++ b/modules/nf-core/tabix/tabix/main.nf @@ -0,0 +1,45 @@ +process TABIX_TABIX { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" + + input: + tuple val(meta), path(tab) + + output: + tuple val(meta), path("*.tbi"), optional:true, emit: tbi + tuple val(meta), path("*.csi"), optional:true, emit: csi + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + """ + tabix \\ + --threads $task.cpus \\ + $args \\ + $tab + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + + stub: + """ + touch ${tab}.tbi + touch ${tab}.csi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml new file mode 100644 index 0000000..7864832 --- /dev/null +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -0,0 +1,58 @@ +name: tabix_tabix +description: create tabix index from a sorted bgzip tab-delimited genome file +keywords: + - index + - tabix + - vcf +tools: + - tabix: + description: Generic indexer for TAB-delimited genome position files. + homepage: https://www.htslib.org/doc/tabix.html + documentation: https://www.htslib.org/doc/tabix.1.html + doi: 10.1093/bioinformatics/btq671 + licence: ["MIT"] + identifier: biotools:tabix +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tab: + type: file + description: TAB-delimited genome position file compressed with bgzip + pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" +output: + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: tabix index file + pattern: "*.{tbi}" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: coordinate sorted index file + pattern: "*.{csi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test new file mode 100644 index 0000000..102b0d7 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -0,0 +1,136 @@ +nextflow_process { + + name "Test Process TABIX_TABIX" + script "modules/nf-core/tabix/tabix/main.nf" + process "TABIX_TABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/tabix" + + test("sarscov2_bedgz_tbi") { + config "./tabix_bed.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_bed' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name + ).match() } + ) + } + } + + test("sarscov2_gff_tbi") { + config "./tabix_gff.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_gff' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name).match() } + ) + } + + } + + test("sarscov2_vcf_tbi") { + config "./tabix_vcf_tbi.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_vcf' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2_vcf_csi") { + config "./tabix_vcf_csi.config" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.csi[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2_vcf_csi_stub") { + config "./tabix_vcf_csi.config" + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi_stub' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.csi[0][1]).name + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap new file mode 100644 index 0000000..c2b9ed0 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -0,0 +1,212 @@ +{ + "sarscov2_gff_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "genome.gff3.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:25.653807564" + }, + "sarscov2_bedgz_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.bed.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:09.754082161" + }, + "sarscov2_vcf_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:40.042648294" + }, + "sarscov2_vcf_csi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:07:08.700367261" + }, + "sarscov2_vcf_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" + ] + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:55.362067748" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config new file mode 100644 index 0000000..7ff0590 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_bed.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p bed' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config new file mode 100644 index 0000000..20c0a1e --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_gff.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p gff' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config new file mode 100644 index 0000000..eb4f2d7 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config new file mode 100644 index 0000000..2774c8a --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml new file mode 100644 index 0000000..6eda065 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/tabix: + - "modules/nf-core/tabix/tabix/**" diff --git a/subworkflows/local/utils_nfcore_vcftomat_pipeline/main.nf b/subworkflows/local/utils_nfcore_vcftomat_pipeline/main.nf index 9cc2742..a581c81 100644 --- a/subworkflows/local/utils_nfcore_vcftomat_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_vcftomat_pipeline/main.nf @@ -75,21 +75,13 @@ workflow PIPELINE_INITIALISATION { Channel .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + meta, vcf_path, vcf_index_path -> + if (!vcf_index_path) { + return [ meta + [ to_index:true ] , [ vcf_path ] ] } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + return [ meta + [ to_index:false ] , [ vcf_path, vcf_index_path ] ] } } - .groupTuple() - .map { samplesheet -> - validateInputSamplesheet(samplesheet) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } .set { ch_samplesheet } emit: @@ -205,6 +197,7 @@ def toolCitationText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", + "MultiQC (Ewels et al. 2016)", "." ].join(' ').trim() @@ -217,6 +210,7 @@ def toolBibliographyText() { // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " ].join(' ').trim() diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 0000000..295384c --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,36 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ + +params { + // Base directory for nf-core/modules test data + // modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' + + // Base directory for nf-core/rnaseq test data + pipelines_testdata_base_path = '${projectDir}/tests/' + + // TODO: check if we rather do this or disable publishdir for all processes when testing modules/subworkflows + outdir = 'testing' +} + +// Impose sensible resource limits for testing +process { + withName: '.*' { + cpus = 2 + memory = 3.GB + time = 2.h + } +} + +// Impose same minimum Nextflow version as the pipeline for testing +manifest { + nextflowVersion = '!>=24.04.2' +} + +// Disable all Nextflow reporting options +timeline { enabled = false } +report { enabled = false } +trace { enabled = false } +dag { enabled = false } diff --git a/workflows/vcftomat.nf b/workflows/vcftomat.nf index a346ca7..35f0b24 100644 --- a/workflows/vcftomat.nf +++ b/workflows/vcftomat.nf @@ -25,8 +25,11 @@ workflow VCFTOMAT { take: ch_samplesheet // channel: samplesheet read in from --input - main: + fasta + fai + dict + main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() @@ -237,6 +240,7 @@ workflow VCFTOMAT { ) emit: + csv = VCF2MAT.out.csv // channel: *.csv multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ]