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40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process AMPS {
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hops=0.35" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
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'quay.io/biocontainers/hops:0.35--hdfd78af_1' }"
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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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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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"""
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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 $task.cpus \\
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-j \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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amps: \$(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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