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