nf-core_modules/modules/samtools/index/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process SAMTOOLS_INDEX {
tag "$meta.id"
label 'process_low'
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publishDir "${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']) }
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conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
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} else {
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
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}
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
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path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
samtools index $options.args $bam
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echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
"""
}