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44 lines
1.4 KiB
Plaintext
44 lines
1.4 KiB
Plaintext
process MACREL_CONTIGS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0':
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'quay.io/biocontainers/macrel:1.1.0--py36hc5360cc_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*/*.smorfs.faa.gz") , emit: smorfs
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tuple val(meta), path("*/*.all_orfs.faa.gz") , emit: all_orfs
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tuple val(meta), path("*/*.prediction.gz") , emit: amp_prediction
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tuple val(meta), path("*/*.md") , emit: readme_file
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tuple val(meta), path("*/*_log.txt") , emit: log_file
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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 ?: "${meta.id}"
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"""
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macrel contigs \\
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$args \\
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--fasta $fasta \\
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--output ${prefix}/ \\
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--tag ${prefix} \\
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--log-file ${prefix}/${prefix}_log.txt \\
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--threads $task.cpus
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gzip --no-name ${prefix}/*.faa
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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macrel: \$(echo \$(macrel --version | sed 's/macrel //g'))
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END_VERSIONS
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"""
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}
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