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https://github.com/MillironX/nf-core_modules.git
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c29b3fe11a
* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads * Corrected fgbio call container, trying to fix fgbio group tests * Removed incorrect line
35 lines
1 KiB
Text
35 lines
1 KiB
Text
process FGBIO_CALLMOLECULARCONSENSUSREADS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
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'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
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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("*.bam"), emit: bam
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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 prefix = task.ext.prefix ?: "${meta.id}"
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"""
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fgbio \\
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CallMolecularConsensusReads \\
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-i $bam \\
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$args \\
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-o ${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
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END_VERSIONS
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"""
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}
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