Merge branch 'dev' into final-reads-saving
James A. Fellows Yates
1 year ago
committed by
GitHub
commit
0245c4880b
@ -1,56 +0,0 @@
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process SAMTOOLS_BAM2FQ {
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tag "$meta.id"
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label 'process_low'
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conda "bioconda::samtools=1.16.1"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
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'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
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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 | gzip --no-name > ${prefix}_interleaved.fq.gz
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cat <<-END_VERSIONS > versions.yml
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"${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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@ -0,0 +1,44 @@
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process SAMTOOLS_FASTQ {
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tag "$meta.id"
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label 'process_low'
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conda "bioconda::samtools=1.16.1"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
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'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
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input:
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tuple val(meta), path(input)
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val(interleave)
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output:
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tuple val(meta), path("*_{1,2}.fastq.gz") , optional:true, emit: fastq
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tuple val(meta), path("*_interleaved.fastq.gz"), optional:true, emit: interleaved
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tuple val(meta), path("*_singleton.fastq.gz") , optional:true, emit: singleton
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tuple val(meta), path("*_other.fastq.gz") , optional:true, emit: other
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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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def output = ( interleave && ! meta.single_end ) ? "> ${prefix}_interleaved.fastq.gz" :
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meta.single_end ? "-1 ${prefix}_1.fastq.gz -s ${prefix}_singleton.fastq.gz" :
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"-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz -s ${prefix}_singleton.fastq.gz"
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"""
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samtools \\
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fastq \\
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$args \\
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--threads ${task.cpus-1} \\
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-0 ${prefix}_other.fastq.gz \\
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$input \\
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$output
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cat <<-END_VERSIONS > versions.yml
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"${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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@ -0,0 +1,62 @@
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name: samtools_fastq
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description: Converts a SAM/BAM/CRAM file to FASTQ
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keywords:
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- bam
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- sam
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- cram
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- fastq
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: http://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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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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- input:
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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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- interleave:
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type: boolean
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description: Set true for interleaved fastq file
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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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- fastq:
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type: file
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description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.
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pattern: "*_{1,2}.fastq.gz"
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- interleaved:
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type: file
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description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
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pattern: "*_interleaved.fastq.gz"
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- singleton:
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type: file
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description: Compressed FASTQ file with singleton reads
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pattern: "*_singleton.fastq.gz"
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- other:
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type: file
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description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset
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pattern: "*_other.fastq.gz"
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authors:
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- "@priyanka-surana"
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- "@suzannejin"
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