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90aef30f43
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
process ENTREZDIRECT_ESUMMARY {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/entrez-direct:16.2--he881be0_1':
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'quay.io/biocontainers/entrez-direct:16.2--he881be0_1' }"
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input:
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tuple val(meta), val(uid), path(uids_file)
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val database
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output:
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tuple val(meta), path("*.xml"), emit: xml
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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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input = uids_file ? "-input ${uids_file}" : "-id ${uid}"
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if (!uid && !uids_file) error "No input. Valid input: an identifier or a .txt file with identifiers"
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if (uid && uids_file) error "Only one input is required: a single identifier or a .txt file with identifiers"
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"""
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esummary \\
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$args \\
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-db $database \\
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$input > ${prefix}.xml
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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esummary: \$(esummary -version)
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END_VERSIONS
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"""
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}
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