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f93c2f2604
* add Krona_db module * removed md5 sum * Update tests/modules/kronatools/kronadb/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * added input information * removed trailing white spaces * changed krona version to 2.7.1 * Apply suggestions from code review * Update modules/kronatools/kronadb/meta.yml * Update modules/kronatools/kronadb/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
35 lines
1.1 KiB
Text
35 lines
1.1 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 KRONATOOLS_KRONADB {
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5"
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} else {
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container "quay.io/biocontainers/krona:2.7.1--pl526_5"
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}
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input:
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output:
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path 'taxonomy/taxonomy.tab', emit: db
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path "versions.yml" , emit: versions
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script:
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def VERSION='2.7.1'
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"""
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ktUpdateTaxonomy.sh taxonomy
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: $VERSION
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END_VERSIONS
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"""
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}
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