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3868c3ab4b
* initial commit [ci skip] * reuse the modules code from nf-core/mag [ci skip] * add contextual information for the module [ci skip] * add stubs to avoid downloading db [ci skip] * trigger test * iterate on tests [ci skip] * itereate tests [ci skip] * add bins [ci skip] * fix stubs [ci skip] * interation on tests with stubs [ci skip] * use the existing pattern and fasta for input * accomodate the new version file format * use variable for the stub [ci skip] * update the versions file in meta.yml * Accomodate code review regarding publishDir function [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * remove extra newline * use bioconda channel * update the description for filtered file * Apply suggestions from code review * Update main.nf * Update main.nf * Update modules/gtdbtk/classifywf/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
32 lines
887 B
Text
32 lines
887 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GTDBTK_CLASSIFYWF } from '../../../../modules/gtdbtk/classifywf/main.nf' addParams( options: [:] )
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process STUB_GTDBTK_DATABASE {
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output:
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tuple val("gtdbtk_r202_data"), path("database/*"), emit: database
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stub:
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"""
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mkdir database
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touch database/gtdbtk_r202_data
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"""
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}
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workflow test_gtdbtk_classifywf {
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STUB_GTDBTK_DATABASE()
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input = [
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[ id:'test', single_end:false, assembler:'SPADES' ],
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[
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
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]
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]
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GTDBTK_CLASSIFYWF ( input, STUB_GTDBTK_DATABASE.out.database )
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}
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