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9d7208504d
* Add gecco/run module * Fix container URLs * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
47 lines
1.4 KiB
Text
47 lines
1.4 KiB
Text
process GECCO_RUN {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gecco=0.9.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gecco:0.9.2--pyhdfd78af_0':
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'quay.io/biocontainers/gecco:0.9.2--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(hmm)
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path model_dir
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output:
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tuple val(meta), path("*.genes.tsv") , emit: genes
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tuple val(meta), path("*.features.tsv") , emit: features
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tuple val(meta), path("*.clusters.tsv") , emit: clusters
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tuple val(meta), path("*_cluster_*.gbk"), optional: true, emit: gbk
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tuple val(meta), path("*.json") , optional: true, emit: json
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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 custom_model = model_dir ? "--model ${model_dir}" : ""
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def custom_hmm = hmm ? "--hmm ${hmm}" : ""
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"""
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gecco \\
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run \\
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$args \\
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-j $task.cpus \\
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-o ./ \\
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-g ${input} \\
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$custom_model \\
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$custom_hmm
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gecco: \$(echo \$(gecco --version) | cut -f 2 -d ' ' )
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END_VERSIONS
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"""
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}
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