diff --git a/tests/modules/krona/ktimporttaxonomy/main.nf b/tests/modules/krona/ktimporttaxonomy/main.nf index 280658a5..e58543a6 100644 --- a/tests/modules/krona/ktimporttaxonomy/main.nf +++ b/tests/modules/krona/ktimporttaxonomy/main.nf @@ -2,9 +2,11 @@ nextflow.enable.dsl = 2 -include { KRONA_KTIMPORTTAXONOMY_READS } from '../../../../modules/krona/ktimporttaxonomy/main.nf' +include { KRONA_KTIMPORTTAXONOMY as TAXONOMY_READS } from '../../../../modules/krona/ktimporttaxonomy/main.nf' -include { KRONA_KTIMPORTTAXONOMY_REPORT } from '../../../../modules/krona/ktimporttaxonomy/main.nf' +include { KRONA_KTIMPORTTAXONOMY as TAXONOMY_REPORT } from '../../../../modules/krona/ktimporttaxonomy/main.nf' + +include { KRONA_KRONADB as DOWNLOAD_DB } from '../../../../modules/krona/kronadb/main.nf' workflow test_krona_ktimporttaxonomy_reads { @@ -12,9 +14,10 @@ workflow test_krona_ktimporttaxonomy_reads { [ id:'test', single_end:false ], // meta map file(params.test_data['sarscov2']['metagenome']['test_1.kraken2.reads.txt'], checkIfExists: true) ] - taxonomy = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) + // taxonomy = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) - KRONA_KTIMPORTTAXONOMY_READS ( input, taxonomy ) + DOWNLOAD_DB() + TAXONOMY_READS ( input, DOWNLOAD_DB.out.db ) } workflow test_krona_ktimporttaxonomy_report { @@ -25,5 +28,6 @@ workflow test_krona_ktimporttaxonomy_report { ] taxonomy = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) - KRONA_KTIMPORTTAXONOMY_REPORT ( input, taxonomy ) + TDOWNLOAD_DB() + TAXONOMY_REPORT ( input, DOWNLOAD_DB.out.db ) }