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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process AMPS {
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::hops=0.35" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
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} else {
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container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
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}
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input:
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path maltextract_results
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path taxon_list
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val filter
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output:
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path "results/heatmap_overview_Wevid.json" , emit: json
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path "results/heatmap_overview_Wevid.pdf" , emit: summary_pdf
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path "results/heatmap_overview_Wevid.tsv" , emit: tsv
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path "results/pdf_candidate_profiles/" , emit: candidate_pdfs
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path "versions.yml" , emit: versions
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script:
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"""
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postprocessing.AMPS.r \\
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-r $maltextract_results \\
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-n $taxon_list \\
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-m $filter \\
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-t $task.cpus \\
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-j \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(hops --version 2>&1) | sed 's/HOPS version//')
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END_VERSIONS
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"""
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}
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