nf-core_modules/software/samtools/stats/main.nf
Jose Espinosa-Carrasco 572abb00b3
Remove def from module options definition in main (#270)
* Remove def from module options definition in main

* Fix bismark_deduplicate tests

* Fix bwameth_align tests

* Fixing gatk4 conda tests ("=" instead of ':' in build id)

* Same as previous commit (Fix gatk4 test)

* Fix qualimap bamqc test (no md5 check for pngs)

* Fix seqkit split2 tests. Changed to new test data

* Fix samtools tests. Some were missing initOptions include

* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00

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Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SAMTOOLS_STATS {
tag "$meta.id"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
} else {
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
}
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
"""
}