mirror of
https://github.com/MillironX/nf-core_modules.git
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eae945721d
* not working yet (db not found)
* modify deeparg/download module to return db-path
* 🪄
* Prettier
* add test.yml
* much prettier
* test.yml delete md5 for pot. empty files
* adapt test.yml
* test.yml again
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
33 lines
1 KiB
Text
33 lines
1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GUNZIP } from '../../../modules/gunzip/main.nf'
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include { PRODIGAL } from '../../../modules/prodigal/main.nf'
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include { DEEPBGC_DOWNLOAD } from '../../../../modules/deepbgc/download/main.nf'
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include { DEEPBGC_PIPELINE } from '../../../../modules/deepbgc/pipeline/main.nf'
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workflow test_deepbgc_pipeline_gbk {
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input = [
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[ id:'test_gbk', single_end:false ], // meta map
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
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]
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DEEPBGC_DOWNLOAD ()
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GUNZIP ( input )
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PRODIGAL ( GUNZIP.out.gunzip, 'gbk' )
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DEEPBGC_PIPELINE ( PRODIGAL.out.gene_annotations, DEEPBGC_DOWNLOAD.out.db )
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}
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workflow test_deepbgc_pipeline_fa {
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input = [
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[ id:'test_fa', single_end:false ], // meta map
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
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]
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DEEPBGC_DOWNLOAD ()
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GUNZIP ( input )
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DEEPBGC_PIPELINE ( GUNZIP.out.gunzip, DEEPBGC_DOWNLOAD.out.db )
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}
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