nf-core_modules/modules/samtools/view/main.nf
Gregor Sturm 906577873b
Bulk update modules to use versions.yml (#739)
* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:41:24 +01:00

38 lines
1.4 KiB
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=1.13' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
} else {
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
}
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
samtools view $options.args $bam > ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}