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https://github.com/MillironX/nf-core_modules.git
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d1c6082a66
* Update HISAT2 build module * Bump preseq version * Fix tests * Add meta.yml for preseq to fix linting * Auto-detect --genomeSAindexNbases for smaller genomes * Add placeholder to use human data for the tests * Add CSI output option to samtools/index * Fix samtools/index tests
35 lines
1.2 KiB
Text
35 lines
1.2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process SAMTOOLS_INDEX {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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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=1.10" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
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} else {
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container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
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}
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.bai"), optional:true, emit: bai
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tuple val(meta), path("*.csi"), optional:true, emit: csi
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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samtools index $options.args $bam
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echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
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"""
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}
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