From da82e06354c34bf6381a86e5af195b24d7ef98ee Mon Sep 17 00:00:00 2001 From: Lucpen <luci9393@hotmail.com> Date: Mon, 2 May 2022 14:16:07 +0200 Subject: [PATCH] fix gatk4_mutect2 test --- tests/modules/gatk4/mutect2/main.nf | 14 +++++++++----- tests/modules/gatk4/mutect2/test.yml | 5 +++-- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf index 251e1987..486b78ad 100644 --- a/tests/modules/gatk4/mutect2/main.nf +++ b/tests/modules/gatk4/mutect2/main.nf @@ -119,10 +119,14 @@ workflow test_gatk4_mutect2_mitochondria { GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] ) } -workflow test_gatk4_mutect2_tumor_single_stubs { - input = [ [ id:'test'], // meta map - [ "foo.bam" ], - [ "foo.bam.bai" ], +workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs { + input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map + [ "foo_parired.bam", + "foo_parired2.bam" + ], + [ "foo_parired.bam.bai", + "foo_parired2.bam.bai" + ], [] ] @@ -134,5 +138,5 @@ workflow test_gatk4_mutect2_tumor_single_stubs { panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz" panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi" - GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } diff --git a/tests/modules/gatk4/mutect2/test.yml b/tests/modules/gatk4/mutect2/test.yml index 9232cedd..3853801d 100644 --- a/tests/modules/gatk4/mutect2/test.yml +++ b/tests/modules/gatk4/mutect2/test.yml @@ -70,12 +70,13 @@ - path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/versions.yml -- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single_stubs - command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run +- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs + command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run tags: - gatk4 - gatk4/mutect2 files: + - path: output/gatk4/test.f1r2.tar.gz - path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz.stats - path: output/gatk4/test.vcf.gz.tbi