Update for mutect2: add output channel for stats file (#716)

* added output channel for stats file, updated meta yml with description and test yml with check for stats file

* Update modules/gatk4/mutect2/main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/gatk4/mutect2/main.nf

@@ -31,10 +31,11 @@ process GATK4_MUTECT2 {
     path panel_of_normals_idx
 
     output:
-    tuple val(meta), path("*.vcf.gz"), emit: vcf
-    tuple val(meta), path("*.tbi")   , emit: tbi
+    tuple val(meta), path("*.vcf.gz")     , emit: vcf
+    tuple val(meta), path("*.tbi")        , emit: tbi
+    tuple val(meta), path("*.stats")      , emit: stats
     tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2
-    path "*.version.txt"          , emit: version
+    path "*.version.txt"                  , emit: version
 
     script:
     def software = getSoftwareName(task.process)

modules/gatk4/mutect2/meta.yml

@@ -76,6 +76,10 @@ output:
       type: file
       description: Index of vcf file
       pattern: "*vcf.gz.tbi"
+  - stats:
+      type: file
+      description: Stats file that pairs with output vcf file
+      pattern: "*vcf.gz.stats"
   - f1r2:
       type: file
       description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)

tests/modules/gatk4/mutect2/test.yml

@@ -6,6 +6,8 @@
   files:
     - path: output/gatk4/test.f1r2.tar.gz
     - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: 6ecb874e6a95aa48233587b876c2a7a9
     - path: output/gatk4/test.vcf.gz.tbi
 
 - name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
@@ -15,6 +17,8 @@
     - gatk4/mutect2
   files:
     - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: e7ef613f7d158b8a0adf44abe5db2029
     - path: output/gatk4/test.vcf.gz.tbi
 
 - name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
@@ -24,4 +28,6 @@
     - gatk4/mutect2
   files:
     - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+      md5sum: 4f77301a125913170b8e9e7828b4ca3f
     - path: output/gatk4/test.vcf.gz.tbi