nf-core_modules/modules/samtools/flagstat/main.nf
Harshil Patel c5235a983d
nf-core modules bump-versions for all modules (#630)
* Add blacklist of modules that shouldn't be updated to .nf-core.yml

* nf-core modules bump-versions for all modules

* Remove TODO statements identified by linting

* Fix md5sums for failing tests

* Fix more tests
2021-07-28 09:10:44 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SAMTOOLS_FLAGSTAT {
tag "$meta.id"
label 'process_low'
publishDir "${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), path(bai)
output:
tuple val(meta), path("*.flagstat"), emit: flagstat
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
samtools flagstat $bam > ${bam}.flagstat
echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
"""
}