Change mutect config to only have one CALCULATECONTAMINATION statement

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

Author: famosab

conf/modules/mutect2.config

@@ -57,7 +57,7 @@ process {
             ext.prefix = { "${meta.id}.mutect2" }
             publishDir = [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/variant_calling/mutect2/${meta.id}" },
+                path: { params.joint_mutect2 ? "${params.outdir}/variant_calling/mutect2/${meta.patient}" : "${params.outdir}/variant_calling/mutect2/${meta.id}" },
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -99,11 +99,4 @@ process {
             ]
         }
 
-            withName: 'CALCULATECONTAMINATION' {
-                publishDir = [
-                    mode: params.publish_dir_mode,
-                    path: { "${params.outdir}/variant_calling/mutect2/${meta.patient}" },
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
 }