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32 lines
1.4 KiB
Text
32 lines
1.4 KiB
Text
process SAMTOOLS_INDEX {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
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'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*.bam" , includeInputs:true), path("*.bai") , optional:true, emit: bam_bai
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tuple val(meta), path("*.bai") , optional:true, emit: bai
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tuple val(meta), path("*.bam" , includeInputs:true), path("*.csi") , optional:true, emit: bam_csi
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tuple val(meta), path("*.csi") , optional:true, emit: csi
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tuple val(meta), path("*.cram", includeInputs:true), path("*.crai"), optional:true, emit: cram_crai
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tuple val(meta), path("*.crai") , optional:true, emit: crai
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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"""
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samtools index -@ ${task.cpus-1} $args $input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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