From 771425e7a050acf0e1be41d9e6fc800f675c3e58 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 7 Jun 2022 12:11:18 +0200
Subject: [PATCH 1/2] add threads to calibratedragstrmodel

---
 modules/gatk4/calibratedragstrmodel/main.nf        |  1 +
 tests/modules/gatk4/calibratedragstrmodel/test.yml | 12 ++++++------
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/modules/gatk4/calibratedragstrmodel/main.nf b/modules/gatk4/calibratedragstrmodel/main.nf
index 08ba7008..b4e47edc 100644
--- a/modules/gatk4/calibratedragstrmodel/main.nf
+++ b/modules/gatk4/calibratedragstrmodel/main.nf
@@ -38,6 +38,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
         --output ${prefix}.txt \\
         --reference $fasta \\
         --str-table-path $strtablefile \\
+        --threads $task.cpus \\
         $intervals_command \\
         --tmp-dir . \\
         $args
diff --git a/tests/modules/gatk4/calibratedragstrmodel/test.yml b/tests/modules/gatk4/calibratedragstrmodel/test.yml
index 53c428a9..285d04ca 100644
--- a/tests/modules/gatk4/calibratedragstrmodel/test.yml
+++ b/tests/modules/gatk4/calibratedragstrmodel/test.yml
@@ -1,26 +1,26 @@
 - name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam
   command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_bam -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
   tags:
-    - gatk4/calibratedragstrmodel
     - gatk4
+    - gatk4/calibratedragstrmodel
   files:
     - path: output/gatk4/test.txt
-      md5sum: 0a1a1583b157fa2251dd931ed165da4f
+      md5sum: e16fa32906c74bb18b93e98a86718ff1
 
 - name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram
   command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_cram -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
   tags:
-    - gatk4/calibratedragstrmodel
     - gatk4
+    - gatk4/calibratedragstrmodel
   files:
     - path: output/gatk4/test.txt
-      md5sum: 1aa7ab38023f724877b3323c5e6b9a4e
+      md5sum: 81c7bf338886cb4d5c2cc07fc56afe44
 
 - name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_beds
   command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_beds -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
   tags:
-    - gatk4/calibratedragstrmodel
     - gatk4
+    - gatk4/calibratedragstrmodel
   files:
     - path: output/gatk4/test.txt
-      md5sum: def8baccad7bd59006f08fcb0a6721bf
+      md5sum: cb6a9acdee042302b54fd1f59b5f54ee

From 4c7ef30fb64f75ba4499d3b8fba24a068b1ce586 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 7 Jun 2022 12:17:14 +0200
Subject: [PATCH 2/2] changed to label to medium

---
 modules/gatk4/calibratedragstrmodel/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gatk4/calibratedragstrmodel/main.nf b/modules/gatk4/calibratedragstrmodel/main.nf
index b4e47edc..37a54de4 100644
--- a/modules/gatk4/calibratedragstrmodel/main.nf
+++ b/modules/gatk4/calibratedragstrmodel/main.nf
@@ -1,6 +1,6 @@
 process GATK4_CALIBRATEDRAGSTRMODEL {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?