diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f8fc243..de0411ea 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` +| Tool | Previous version | New version | +| ------------- | ---------------- | ----------- | +| AMRFinderPlus | 3.10.42 | 3.11.18 | +| Bakta | 1.7.0 | 1.8.2 | +| MultiQC | 1.1.4 | 1.1.5 | + ### `Deprecated` ## v1.1.3 - [2023-08-11] diff --git a/modules.json b/modules.json index 2d47f5a7..584b643a 100644 --- a/modules.json +++ b/modules.json @@ -27,12 +27,12 @@ }, "amrfinderplus/run": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "016547e536216e0e839eb8ec678d13b25211c174", "installed_by": ["modules"] }, "amrfinderplus/update": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "868d4c3dc7a3db39d36184173e4fe3484499396e", "installed_by": ["modules"] }, "antismash/antismashlite": { @@ -47,12 +47,12 @@ }, "bakta/bakta": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880", "installed_by": ["modules"] }, "bakta/baktadbdownload": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "f05fa7c6753f92be861d606378860dcd5c828880", "installed_by": ["modules"] }, "bioawk": { @@ -63,7 +63,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "deeparg/downloaddata": { @@ -91,11 +91,6 @@ "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, - "fastqc": { - "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", - "installed_by": ["modules"] - }, "gecco/run": { "branch": "master", "git_sha": "8c029dd8e67754d937fb6b6814e568f1decb2fea", @@ -148,7 +143,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", "installed_by": ["modules"] }, "prodigal": { diff --git a/modules/nf-core/amrfinderplus/run/main.nf b/modules/nf-core/amrfinderplus/run/main.nf index 8077bb48..f178b68f 100644 --- a/modules/nf-core/amrfinderplus/run/main.nf +++ b/modules/nf-core/amrfinderplus/run/main.nf @@ -2,10 +2,10 @@ process AMRFINDERPLUS_RUN { tag "$meta.id" label 'process_medium' - conda "bioconda::ncbi-amrfinderplus=3.10.42" + conda "bioconda::ncbi-amrfinderplus=3.11.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0': - 'biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }" + 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0': + 'biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }" input: tuple val(meta), path(fasta) @@ -23,7 +23,8 @@ process AMRFINDERPLUS_RUN { script: def args = task.ext.args ?: '' - def is_compressed = fasta.getName().endsWith(".gz") ? true : false + def is_compressed_fasta = fasta.getName().endsWith(".gz") ? true : false + def is_compressed_db = db.getName().endsWith(".gz") ? true : false prefix = task.ext.prefix ?: "${meta.id}" organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : "" fasta_name = fasta.getName().replace(".gz", "") @@ -34,12 +35,16 @@ process AMRFINDERPLUS_RUN { } } """ - if [ "$is_compressed" == "true" ]; then + if [ "$is_compressed_fasta" == "true" ]; then gzip -c -d $fasta > $fasta_name fi - mkdir amrfinderdb - tar xzvf $db -C amrfinderdb + if [ "$is_compressed_db" == "true" ]; then + mkdir amrfinderdb + tar xzvf $db -C amrfinderdb + else + mv $db amrfinderdb + fi amrfinder \\ $fasta_param $fasta_name \\ diff --git a/modules/nf-core/amrfinderplus/update/main.nf b/modules/nf-core/amrfinderplus/update/main.nf index a043a06a..bf3c5ef6 100644 --- a/modules/nf-core/amrfinderplus/update/main.nf +++ b/modules/nf-core/amrfinderplus/update/main.nf @@ -2,10 +2,10 @@ process AMRFINDERPLUS_UPDATE { tag "update" label 'process_single' - conda "bioconda::ncbi-amrfinderplus=3.10.42" + conda "bioconda::ncbi-amrfinderplus=3.11.18" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.42--h6e70893_0': - 'biocontainers/ncbi-amrfinderplus:3.10.42--h6e70893_0' }" + 'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.18--h283d18e_0': + 'biocontainers/ncbi-amrfinderplus:3.11.18--h283d18e_0' }" output: path "amrfinderdb.tar.gz", emit: db @@ -17,9 +17,8 @@ process AMRFINDERPLUS_UPDATE { script: def args = task.ext.args ?: '' """ - mkdir amrfinderdb amrfinder_update -d amrfinderdb - tar czvf amrfinderdb.tar.gz -C \$(readlink amrfinderdb/latest) ./ + tar czvf amrfinderdb.tar.gz -C amrfinderdb/\$(readlink amrfinderdb/latest) ./ cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf index 6399f5d0..fd0b76f2 100644 --- a/modules/nf-core/bakta/bakta/main.nf +++ b/modules/nf-core/bakta/bakta/main.nf @@ -2,10 +2,10 @@ process BAKTA_BAKTA { tag "$meta.id" label 'process_medium' - conda "bioconda::bakta=1.7.0" + conda "bioconda::bakta=1.8.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' : - 'biocontainers/bakta:1.7.0--pyhdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' : + 'biocontainers/bakta:1.8.2--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bakta/baktadbdownload/main.nf b/modules/nf-core/bakta/baktadbdownload/main.nf index e62a2bed..de7e2199 100644 --- a/modules/nf-core/bakta/baktadbdownload/main.nf +++ b/modules/nf-core/bakta/baktadbdownload/main.nf @@ -1,10 +1,10 @@ process BAKTA_BAKTADBDOWNLOAD { label 'process_single' - conda "bioconda::bakta=1.7.0" + conda "bioconda::bakta=1.8.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' : - 'biocontainers/bakta:1.7.0--pyhdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/bakta:1.8.2--pyhdfd78af_0' : + 'biocontainers/bakta:1.8.2--pyhdfd78af_0' }" output: path "db*" , emit: db diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index 249f9064..00000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,55 +0,0 @@ -process FASTQC { - tag "$meta.id" - label 'process_medium' - - conda "bioconda::fastqc=0.11.9" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - $args \\ - --threads $task.cpus \\ - $renamed_files - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index 4da5bb5a..00000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,52 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] -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. -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..65d7dd0d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*"