mirror of
https://github.com/MillironX/nf-core_modules.git
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e9bc33485e
* bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list
* Added a test
* Added a test
* Added MD5 checksum
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
56 lines
1.8 KiB
Text
56 lines
1.8 KiB
Text
process SAMTOOLS_MERGE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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input:
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tuple val(meta), path(input_files, stageAs: "?/*")
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path fasta
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path fai
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output:
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tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
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tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
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tuple val(meta), path("*.csi") , optional:true, emit: csi
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
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def reference = fasta ? "--reference ${fasta}" : ""
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"""
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samtools \\
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merge \\
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--threads ${task.cpus-1} \\
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$args \\
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${reference} \\
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${prefix}.${file_type} \\
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$input_files
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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stub:
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
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"""
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touch ${prefix}.${file_type}
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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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