diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 858e7737..e8729b9b 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -135,6 +135,7 @@ params { test_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" test_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" test_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" + test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" diff --git a/tests/modules/optitype/main.nf b/tests/modules/optitype/main.nf index 7d740473..c27a5c99 100644 --- a/tests/modules/optitype/main.nf +++ b/tests/modules/optitype/main.nf @@ -6,8 +6,8 @@ include { OPTITYPE } from '../../../modules/optitype/main.nf' addParams( options workflow test_optitype { input = [ [ id:'test', seq_type:'dna' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla'], checkIfExists: true) ] - + OPTITYPE ( input ) } diff --git a/tests/modules/optitype/test.yml b/tests/modules/optitype/test.yml index 5ee5a067..41f35988 100644 --- a/tests/modules/optitype/test.yml +++ b/tests/modules/optitype/test.yml @@ -3,5 +3,7 @@ tags: - optitype files: - - path: output/optitype/test/test_result.tsv - path: output/optitype/test/test_coverage_plot.pdf + - path: output/optitype/test/test_result.tsv + contains: + - '1446'