nf-core_modules/modules/samtools/view/main.nf
FriederikeHanssen 19035c99d1
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>
2021-11-18 22:24:47 +01:00

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Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SAMTOOLS_VIEW {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
} else {
container "quay.io/biocontainers/samtools:1.14--hb421002_0"
}
input:
tuple val(meta), path(input)
path fasta
output:
tuple val(meta), path("*.bam") , emit: bam , optional: true
tuple val(meta), path("*.cram"), emit: cram, optional: true
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def reference = fasta ? "--reference ${fasta} -C" : ""
def file_type = input.getExtension()
"""
samtools view --threads ${task.cpus-1} ${reference} $options.args $input > ${prefix}.${file_type}
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}