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15fd90ffe8
* initial stubs [ci skip] * remove comments and add main command [ci skip] * design iteration [ci skip] * add new standard functions.nf [ci skip] * update the version string [ci skip] * accomodate the db stubs and single/double ends [ci skip] * add FIXME for missing info [ci skip] * Accomodate the results folder [ci skip] * Update main.nf * Apply suggestions from code review * Update main.nf * Apply suggestions from code review * Add version file to stubs [ci skip] * Tweak the output dir pattern [ci skip] * Update modules/phyloflash/main.nf * Update modules/phyloflash/main.nf * Update modules/phyloflash/main.nf Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
44 lines
1.1 KiB
Text
44 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PHYLOFLASH } from '../../../modules/phyloflash/main.nf' addParams( options: [:] )
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process STUB_PHYLOFLASH_DATABASE {
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output:
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path "ref" , emit: silva_db
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path "UniVec" , emit: univec_db
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stub:
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"""
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mkdir ref
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touch UniVec
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"""
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}
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workflow test_phyloflash_single_end {
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STUB_PHYLOFLASH_DATABASE ()
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input = [
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[ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db, STUB_PHYLOFLASH_DATABASE.out.univec_db )
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}
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workflow test_phyloflash_paired_end {
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STUB_PHYLOFLASH_DATABASE ()
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db, STUB_PHYLOFLASH_DATABASE.out.univec_db )
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}
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