nf-core_modules/software/samtools/stats/main.nf
Maxime U. Garcia 25f88dee3c
Update samtools from 1.10 to 1.12 (#530)
* feat: remove social preview image to use GitHub OpenGraph

* feat: update samtools from 1.10 to 1.12

* fix: CI tests

* fix: add meta.yml file for samtools/merge

* Update software/samtools/merge/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update software/samtools/merge/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-07 13:07:32 +02:00

34 lines
1.2 KiB
Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SAMTOOLS_STATS {
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=1.12" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
} else {
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
}
input:
tuple val(meta), path(bam), path(bai)
output:
tuple val(meta), path("*.stats"), emit: stats
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
samtools stats $bam > ${bam}.stats
echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
"""
}