mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Add thread option to samtools modules (#1069)
* add thread option to samtools modules * fix tests * fix tests * fix tests * Fix naming to fix tests * cpus-1 to account for mainthread * remove thread in ampliconclip, docu doesn't report this param * add -1 to all other applicable samtools modules * Update samtools version * Update checksums * retrigger GHA after update * Update modules/samtools/fastq/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/flagstat/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/index/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/merge/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/stats/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Update modules/samtools/view/main.nf Co-authored-by: Patrick Hüther <patrick.huether@gmail.com> * Fix md5sum fixmate * Fix md5sums * sth funny with the fixmate checksums * more md5sums updates Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
This commit is contained in:
FriederikeHanssen
GitHub
parent
4e5b6ed843
commit
19035c99d1
21 changed files with 79 additions and 76 deletions
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@ -11,11 +11,11 @@ process SAMTOOLS_AMPLICONCLIP {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::samtools=1.13" : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -38,7 +38,6 @@ process SAMTOOLS_AMPLICONCLIP {
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samtools \\
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ampliconclip \\
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$options.args \\
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-@ $task.cpus \\
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$rejects \\
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$stats \\
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-b $bed \\
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@ -11,11 +11,11 @@ process SAMTOOLS_FAIDX {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -11,11 +11,11 @@ process SAMTOOLS_FASTQ {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -23,7 +23,7 @@ process SAMTOOLS_FASTQ {
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output:
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tuple val(meta), path("*.fastq.gz"), emit: fastq
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path "versions.yml" , emit: versions
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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@ -32,7 +32,7 @@ process SAMTOOLS_FASTQ {
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"""
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samtools fastq \\
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$options.args \\
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-@ $task.cpus \\
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--threads ${task.cpus-1} \\
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$endedness \\
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$bam
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cat <<-END_VERSIONS > versions.yml
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@ -33,7 +33,7 @@ process SAMTOOLS_FIXMATE {
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samtools \\
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fixmate \\
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$options.args \\
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-@ $task.cpus \\
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--threads ${task.cpus-1} \\
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$bam \\
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${prefix}.bam \\
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@ -11,11 +11,11 @@ process SAMTOOLS_FLAGSTAT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -27,7 +27,7 @@ process SAMTOOLS_FLAGSTAT {
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script:
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"""
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samtools flagstat $bam > ${bam}.flagstat
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samtools flagstat --threads ${task.cpus-1} $bam > ${bam}.flagstat
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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@ -11,11 +11,11 @@ process SAMTOOLS_IDXSTATS {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -11,11 +11,11 @@ process SAMTOOLS_INDEX {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -29,7 +29,8 @@ process SAMTOOLS_INDEX {
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script:
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"""
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samtools index $options.args $input
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samtools index -@ ${task.cpus-1} $options.args $input
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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@ -11,11 +11,11 @@ process SAMTOOLS_MERGE {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -32,7 +32,8 @@ process SAMTOOLS_MERGE {
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def file_type = input_files[0].getExtension()
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def reference = fasta ? "--reference ${fasta}" : ""
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"""
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samtools merge ${reference} ${prefix}.${file_type} $input_files
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samtools merge --threads ${task.cpus-1} $options.args ${reference} ${prefix}.${file_type} $input_files
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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@ -11,11 +11,11 @@ process SAMTOOLS_MPILEUP {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -11,11 +11,11 @@ process SAMTOOLS_SORT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -11,11 +11,11 @@ process SAMTOOLS_STATS {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -29,7 +29,8 @@ process SAMTOOLS_STATS {
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script:
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def reference = fasta ? "--reference ${fasta}" : ""
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"""
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samtools stats ${reference} ${input} > ${input}.stats
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samtools stats --threads ${task.cpus-1} ${reference} ${input} > ${input}.stats
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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@ -11,11 +11,11 @@ process SAMTOOLS_VIEW {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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container "quay.io/biocontainers/samtools:1.14--hb421002_0"
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}
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input:
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@ -23,16 +23,17 @@ process SAMTOOLS_VIEW {
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path fasta
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output:
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tuple val(meta), path("*.bam") , optional: true, emit: bam
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tuple val(meta), path("*.cram"), optional: true, emit: cram
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.bam") , emit: bam , optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def reference = fasta ? "--reference ${fasta} -C" : ""
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def file_type = input.getExtension()
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"""
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samtools view ${reference} $options.args $input > ${prefix}.${file_type}
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samtools view --threads ${task.cpus-1} ${reference} $options.args $input > ${prefix}.${file_type}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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@ -7,7 +7,7 @@
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- samtools/ampliconclip
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files:
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- path: output/samtools/test.bam
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md5sum: 1c705ebe39f68f1dac164733ae99c9d2
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md5sum: 678f9ab04fbe3206f0f96e170fd833e9
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- name: samtools ampliconclip no stats with rejects
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command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c tests/config/nextflow.config
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@ -16,9 +16,9 @@
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- samtools/ampliconclip
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files:
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- path: output/samtools/test.bam
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md5sum: 86c7bfb5378d57b16855c5b399000b2a
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md5sum: bbf65ea626539d96c8271e17d1fc988b
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- path: output/samtools/test.cliprejects.bam
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md5sum: 8e2eea2c0005b4d4e77c0eb549599133
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md5sum: a0bee15aead020d16d0c81bd9667df46
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- name: samtools ampliconclip with stats with rejects
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command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c tests/config/nextflow.config
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@ -27,8 +27,8 @@
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- samtools/ampliconclip
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files:
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- path: output/samtools/test.bam
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||||
md5sum: d96f5eebef0ff4635e68090e89756d4a
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||||
md5sum: f5a3611ecad34ba2dde77096e1c7dd93
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- path: output/samtools/test.cliprejects.bam
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md5sum: ad83a523d6ff1c58caade4ddafbaaed7
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||||
md5sum: 90ee7ce908b4bdb89ab41e4410de9012
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- path: output/samtools/test.clipstats.txt
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md5sum: 6fbde83d658cd2813b79900d33800d1d
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md5sum: fc23355e1743d47f2541f2cb1a7a0cda
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||||
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@ -1,8 +1,8 @@
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- name: samtools fixmate test_samtools_fixmate
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command: nextflow run tests/modules/samtools/fixmate -entry test_samtools_fixmate -c tests/config/nextflow.config
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tags:
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- samtools/fixmate
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- samtools
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- samtools/fixmate
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files:
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- path: output/samtools/test.bam
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md5sum: 92c8463710cdcaef2010aa02ed9e01fd
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md5sum: a4092657a4b17170c7702a76cbf192a1
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@ -1,4 +1,4 @@
|
|||
- name: samtools index bai
|
||||
- name: samtools index test_samtools_index_bai
|
||||
command: nextflow run tests/modules/samtools/index -entry test_samtools_index_bai -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
|
|
@ -7,7 +7,7 @@
|
|||
- path: output/samtools/test.paired_end.sorted.bam.bai
|
||||
md5sum: 704c10dd1326482448ca3073fdebc2f4
|
||||
|
||||
- name: samtools index crai
|
||||
- name: samtools index test_samtools_index_crai
|
||||
command: nextflow run tests/modules/samtools/index -entry test_samtools_index_crai -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
|
|
@ -16,7 +16,7 @@
|
|||
- path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai
|
||||
md5sum: 537e3d8c937bcc4e34e1cf47cd71d484
|
||||
|
||||
- name: samtools index csi
|
||||
- name: samtools index test_samtools_index_csi
|
||||
command: nextflow run tests/modules/samtools/index -entry test_samtools_index_csi -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
|
|
|
|||
|
|
@ -1,15 +1,15 @@
|
|||
- name: samtools merge test_samtools_merge
|
||||
command: nextflow run tests/modules/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools/merge
|
||||
- samtools
|
||||
- samtools/merge
|
||||
files:
|
||||
- path: output/samtools/test_merged.bam
|
||||
|
||||
- name: samtools merge test_samtools_merge_cram
|
||||
command: nextflow run tests/modules/samtools/merge -entry test_samtools_merge_cram -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools/merge
|
||||
- samtools
|
||||
- samtools/merge
|
||||
files:
|
||||
- path: output/samtools/test_merged.cram
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- samtools/sort
|
||||
files:
|
||||
- path: output/samtools/test.sorted.bam
|
||||
md5sum: bbb2db225f140e69a4ac577f74ccc90f
|
||||
md5sum: 4adc495469724a375d5e1a9f3485e38d
|
||||
|
|
|
|||
|
|
@ -14,9 +14,9 @@ workflow test_samtools_stats {
|
|||
}
|
||||
|
||||
workflow test_samtools_stats_cram {
|
||||
input = [ [ id: 'test' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
|
||||
input = [ [ id: 'test', single_end:true ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,17 +1,17 @@
|
|||
- name: samtools stats test_samtools_stats
|
||||
command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools/stats
|
||||
- samtools
|
||||
files:
|
||||
- path: output/samtools/test.paired_end.sorted.bam.stats
|
||||
md5sum: a7f36cf11fd3bf97e0a0ae29c0627296
|
||||
md5sum: 09146eeecfcae2a84fb8615c86cd8d64
|
||||
|
||||
- name: samtools stats test_samtools_stats_cram
|
||||
command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats_cram -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools/stats
|
||||
- samtools
|
||||
files:
|
||||
- path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
|
||||
md5sum: bd55a1da30028403f4b66dacf7a2a20e
|
||||
md5sum: 62377b29c3f6253e37308a28d13a496d
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@
|
|||
- path: ./output/samtools/test.sorted.bam.idxstats
|
||||
md5sum: e16eb632f7f462514b0873c7ac8ac905
|
||||
- path: ./output/samtools/test.sorted.bam.stats
|
||||
md5sum: 2d837cd72432cd856fca70d33f02ffb5
|
||||
md5sum: d9eb909c2cde69d6ae83999a72d770d7
|
||||
|
||||
- name: align bowtie2 paired-end
|
||||
command: nextflow run ./tests/subworkflows/nf-core/align_bowtie2 -entry test_align_bowtie2_paired_end -c tests/config/nextflow.config
|
||||
|
|
@ -78,4 +78,4 @@
|
|||
- path: ./output/samtools/test.sorted.bam.idxstats
|
||||
md5sum: 29ff2fa56d35b2a47625b8f517f1a947
|
||||
- path: ./output/samtools/test.sorted.bam.stats
|
||||
md5sum: 98aa88a39d26244c89bd4e577953fb48
|
||||
md5sum: d0c7a1a4fbd2c1aed437ca419a9e344f
|
||||
|
|
|
|||
|
|
@ -4,15 +4,15 @@
|
|||
- subworkflows/bam_sort_samtools
|
||||
- subworkflows/bam_stats_samtools
|
||||
# Modules
|
||||
# - samtools
|
||||
# - samtools/index
|
||||
# - samtools/sort
|
||||
# - samtools/stats
|
||||
# - samtools/idxstats
|
||||
# - samtools/flagstat
|
||||
- samtools
|
||||
- samtools/index
|
||||
- samtools/sort
|
||||
- samtools/stats
|
||||
- samtools/idxstats
|
||||
- samtools/flagstat
|
||||
files:
|
||||
- path: ./output/samtools/test.sorted.bam
|
||||
md5sum: e4c77897d6824ce4df486d1b100618af
|
||||
md5sum: 8b56bb7d26ced04112f712250d915aaa
|
||||
- path: ./output/samtools/test.sorted.bam.bai
|
||||
md5sum: a70940ce9ba2e700ec2984e0a6526099
|
||||
# samtools stats
|
||||
|
|
@ -36,7 +36,7 @@
|
|||
# - samtools/flagstat
|
||||
files:
|
||||
- path: ./output/samtools/test.sorted.bam
|
||||
md5sum: bbb2db225f140e69a4ac577f74ccc90f
|
||||
md5sum: 4adc495469724a375d5e1a9f3485e38d
|
||||
- path: ./output/samtools/test.sorted.bam.bai
|
||||
md5sum: 20c91e3a0fd4661d7cb967f40d2486ba
|
||||
# samtools stats
|
||||
|
|
|
|||
Loading…
Reference in a new issue