diff --git a/tests/modules/emboss/seqret/main.nf b/tests/modules/emboss/seqret/main.nf index 2275c6c0..d3c703a2 100644 --- a/tests/modules/emboss/seqret/main.nf +++ b/tests/modules/emboss/seqret/main.nf @@ -3,13 +3,48 @@ nextflow.enable.dsl = 2 include { EMBOSS_SEQRET } from '../../../../modules/emboss/seqret/main.nf' +include { GUNZIP } from '../../../modules/gunzip/main.nf' + +workflow test_emboss_seqret_gb2embl { -workflow test_emboss_seqret { - input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ] - EMBOSS_SEQRET ( input ) + GUNZIP ( input ) + EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'embl' ) +} + +workflow test_emboss_seqret_gb2gff { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) + ] + + GUNZIP ( input ) + EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'gff' ) +} + +workflow test_emboss_seqret_gb2pir { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) + ] + + GUNZIP ( input ) + EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'pir' ) +} + +workflow test_emboss_seqret_gb2fasta { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) + ] + + GUNZIP ( input ) + EMBOSS_SEQRET ( GUNZIP.out.gunzip, 'fasta' ) }