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Fix back to nf-core modules version
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3 changed files with 1 additions and 112 deletions
2
modules/nf-core/modules/samtools/bam2fq/main.nf
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2
modules/nf-core/modules/samtools/bam2fq/main.nf
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@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ {
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bam2fq \\
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$args \\
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-@ $task.cpus \\
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$inputbam > ${prefix}_interleaved.fq.gz
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$inputbam >${prefix}_interleaved.fq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -1,56 +0,0 @@
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process SAMTOOLS_BAM2FQ {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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input:
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tuple val(meta), path(inputbam)
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val split
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output:
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tuple val(meta), path("*.fq.gz"), emit: reads
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if (split){
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"""
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samtools \\
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bam2fq \\
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$args \\
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-@ $task.cpus \\
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-1 ${prefix}_1.fq.gz \\
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-2 ${prefix}_2.fq.gz \\
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-0 ${prefix}_other.fq.gz \\
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-s ${prefix}_singleton.fq.gz \\
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$inputbam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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} else {
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"""
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samtools \\
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bam2fq \\
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$args \\
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-@ $task.cpus \\
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$inputbam >${prefix}_interleaved.fq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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}
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@ -1,55 +0,0 @@
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name: samtools_bam2fq
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description: |
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The module uses bam2fq method from samtools to
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convert a SAM, BAM or CRAM file to FASTQ format
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keywords:
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- bam2fq
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- samtools
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- fastq
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tools:
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- samtools:
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description: Tools for dealing with SAM, BAM and CRAM files
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homepage: None
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documentation: http://www.htslib.org/doc/1.1/samtools.html
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tool_dev_url: None
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doi: ""
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- inputbam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- split:
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type: boolean
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description: |
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TRUE/FALSE value to indicate if reads should be separated into
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/1, /2 and if present other, or singleton.
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Note: choosing TRUE will generate 4 different files.
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Choosing FALSE will produce a single file, which will be interleaved in case
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the input contains paired reads.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- reads:
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type: file
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description: |
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FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
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or a single interleaved .fq.gz file if the user chooses not to split the reads.
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pattern: "*.fq.gz"
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authors:
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- "@lescai"
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