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Remove samtools/bam2fq module

This commit is contained in:
sofstam 2023-03-31 10:28:36 +02:00
parent 8745fc625c
commit 021f5f0a22
3 changed files with 127 additions and 159 deletions

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@ -8,222 +8,301 @@
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}
}

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@ -1,56 +0,0 @@
process SAMTOOLS_BAM2FQ {
tag "$meta.id"
label 'process_low'
conda "bioconda::samtools=1.16.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
input:
tuple val(meta), path(inputbam)
val split
output:
tuple val(meta), path("*.fq.gz"), emit: reads
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}"
if (split){
"""
samtools \\
bam2fq \\
$args \\
-@ $task.cpus \\
-1 ${prefix}_1.fq.gz \\
-2 ${prefix}_2.fq.gz \\
-0 ${prefix}_other.fq.gz \\
-s ${prefix}_singleton.fq.gz \\
$inputbam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} else {
"""
samtools \\
bam2fq \\
$args \\
-@ $task.cpus \\
$inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
}

View file

@ -1,55 +0,0 @@
name: samtools_bam2fq
description: |
The module uses bam2fq method from samtools to
convert a SAM, BAM or CRAM file to FASTQ format
keywords:
- bam2fq
- samtools
- fastq
tools:
- samtools:
description: Tools for dealing with SAM, BAM and CRAM files
homepage: None
documentation: http://www.htslib.org/doc/1.1/samtools.html
tool_dev_url: None
doi: ""
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- inputbam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- split:
type: boolean
description: |
TRUE/FALSE value to indicate if reads should be separated into
/1, /2 and if present other, or singleton.
Note: choosing TRUE will generate 4 different files.
Choosing FALSE will produce a single file, which will be interleaved in case
the input contains paired reads.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- reads:
type: file
description: |
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
or a single interleaved .fq.gz file if the user chooses not to split the reads.
pattern: "*.fq.gz"
authors:
- "@lescai"