nf-core_modules/software/samtools/flagstat/main.nf

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2020-08-05 16:17:47 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
process SAMTOOLS_FLAGSTAT {
tag "$meta.id"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
//container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
conda (params.conda ? "bioconda::samtools=1.10" : null)
input:
tuple val(meta), path(bam), path(bai)
val options
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
"""
}