mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
37 lines
1.3 KiB
Text
37 lines
1.3 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process SAMTOOLS_INDEX {
|
|
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)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bai"), optional:true, emit: bai
|
|
tuple val(meta), path("*.csi"), optional:true, emit: csi
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
"""
|
|
samtools index $options.args $bam
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|