nf-core_modules/tests/modules/deepbgc/pipeline/main.nf
louperelo eae945721d
new module: deepbgc/pipeline (#2014)
* 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>
2022-09-07 14:59:01 +02:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GUNZIP } from '../../../modules/gunzip/main.nf'
include { PRODIGAL } from '../../../modules/prodigal/main.nf'
include { DEEPBGC_DOWNLOAD } from '../../../../modules/deepbgc/download/main.nf'
include { DEEPBGC_PIPELINE } from '../../../../modules/deepbgc/pipeline/main.nf'
workflow test_deepbgc_pipeline_gbk {
input = [
[ id:'test_gbk', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
]
DEEPBGC_DOWNLOAD ()
GUNZIP ( input )
PRODIGAL ( GUNZIP.out.gunzip, 'gbk' )
DEEPBGC_PIPELINE ( PRODIGAL.out.gene_annotations, DEEPBGC_DOWNLOAD.out.db )
}
workflow test_deepbgc_pipeline_fa {
input = [
[ id:'test_fa', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
]
DEEPBGC_DOWNLOAD ()
GUNZIP ( input )
DEEPBGC_PIPELINE ( GUNZIP.out.gunzip, DEEPBGC_DOWNLOAD.out.db )
}