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46 lines
1.5 KiB
Plaintext
46 lines
1.5 KiB
Plaintext
process MOTUS_MERGE {
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tag "$meta.id"
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label 'process_single'
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conda "bioconda::motus=3.0.3"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
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'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(input)
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path db // to stop docker saying it can't find it... would have to have the module in upstream steps anyway
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path profile_version_yml, stageAs: 'profile_version.yml'
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output:
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tuple val(meta), path("*.txt") , optional: true, emit: txt
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tuple val(meta), path("*.biom"), optional: true, emit: biom
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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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def cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}"
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def suffix = task.ext.args?.contains("-B") ? "biom" : "txt"
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"""
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motus \\
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merge \\
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-db $db \\
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${cmd_input} \\
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$args \\
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-o ${prefix}.${suffix}
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## Take version from the mOTUs/profile module output, as cannot reconstruct
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## version without having database staged in this directory.
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VERSION=\$(cat ${profile_version_yml} | grep '/*motus:.*' | sed 's/.*otus: //g')
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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motus: \$VERSION
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END_VERSIONS
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"""
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}
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