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59 lines
1.7 KiB
Text
59 lines
1.7 KiB
Text
process SNAPALIGNER_INDEX {
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tag "$fasta"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
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'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
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input:
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path fasta
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path altcontigfile
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path nonaltcontigfile
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path altliftoverfile
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output:
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path "snap/*" ,emit: index
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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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def altcontigfile_arg = altcontigfile ? '-altContigFile ' + altcontigfile : ''
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def nonaltcontigfile_arg = nonaltcontigfile ? '-nonAltContigFile ' + nonaltcontigfile : ''
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def altliftoverfile_arg = altliftoverfile ? '-altLiftoverFile ' + altliftoverfile : ''
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"""
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mkdir snap
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snap-aligner \\
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index \\
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$fasta \\
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snap \\
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-t${task.cpus} \\
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$altcontigfile_arg \\
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$nonaltcontigfile_arg \\
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$altliftoverfile_arg \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //')
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END_VERSIONS
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"""
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stub:
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"""
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mkdir snap
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echo "Genome" > snap/Genome
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echo "GenomeIndex" > snap/GenomeIndex
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echo "GenomeIndexHash" > snap/GenomeIndexHash
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echo "OverflowTable" > snap/OverflowTable
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/\.\$//')
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END_VERSIONS
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"""
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}
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