Merge pull request #644 from FriederikeHanssen/bwa_args

bwa should use -Y and not -M
nf-core · Jul 17, 2022 · d2388d1 · d2388d1
2 parents e1ae69d + f5f49ea
commit d2388d1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -88,6 +88,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#632](https://github.com/nf-core/sarek/pull/632) - Update `VEP` version to `106.1` and cache up to `106`
 - [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files
 - [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
+- [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
 
 ### Fixed
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -234,7 +234,7 @@ process {
 
     if (params.umi_read_structure) {
         withName: "NFCORE_SAREK:SAREK:CREATE_UMI_CONSENSUS:MAPPING_UMI:BWAMEM.*_MEM" {
-            ext.args         = { "-p -C -M -R ${meta.read_group}" }
+            ext.args         = { "-K 100000000 -p -C -Y -R ${meta.read_group}" }
             ext.args2        = '-bS'
             ext.prefix       = {"${meta.id}.umi_unsorted"}
         }
@@ -276,7 +276,7 @@ process {
 
         withName: "NFCORE_SAREK:SAREK:GATK4_MAPPING:BWAMEM.*_MEM" {
             // Using -B 3 for tumor samples
-            ext.args         = { meta.status == 1 ? "-K 100000000 -M -B 3 -R ${meta.read_group}" : "-K 100000000 -M -R ${meta.read_group}" }
+            ext.args         = { meta.status == 1 ? "-K 100000000 -Y -B 3 -R ${meta.read_group}" : "-K 100000000 -Y -R ${meta.read_group}" }
         }
     }