add selection function back in

Author: FriederikeHanssen

conf/modules/modules.config

@@ -127,7 +127,7 @@ process {
         }
 
         withName: 'TMB' {
-            ext.args = "--sample ${meta.patient}_{meta.tumor_id} "
+            ext.args = { "--sample ${meta.patient}_{meta.sample} " } //sample here is the tumor_id
         }
     }
 }

lib/WorkflowSarek.groovy

@@ -103,38 +103,34 @@ class WorkflowSarek {
 
     public static String getTMBdatabase(String annotation) {
 
-       String dbConfig = "/assets/tmb/snpeff.yml";
-
-    //    switch (annotation) {
-    //        case 'snpeff': dbConfig = "$projectDir/assets/tmb/snpeff.yml";
-    //                        break
-    //        case 'vep': dbConfig = "$projectDir/assets/tmb/vep.yml";
-    //                        break
-    //        //case 'merge': dbConfig = "$projectDir/assets/tmb/merge.yml";
-    //        //                break
-    //    }
+        String dbConfig = "";
+
+        switch (annotation) {
+            case 'snpeff': dbConfig = "/assets/tmb/snpeff.yml";
+                           break
+            case 'vep': dbConfig = "/assets/tmb/vep.yml";
+                           break
+            // default:    log.warn "Please provide a valid annotation tool"
+            //             exit 1, "Unknown tool ${annotation}"
+        }
 
        return dbConfig
     }
 
     public static String getTMBvariantcaller(String variantcaller) {
 
-       String varConfig = "/assets/tmb/strelka.yml";
-
-    //    switch (variantcaller) {
-    //        //case 'deepvariant': varConfig = "$projectDir/assets/tmb/deepvariant.yml";
-    //        //                break
-    //        //case 'freebayes': varConfig = "$projectDir/assets/tmb/freebayes.yml";
-    //        //                break
-    //        //case 'haplotypecaller': varConfig = "$projectDir/assets/tmb/haplotypecaller.yml";
-    //        //                break
-    //        //case 'mpileup': varConfig = "$projectDir/assets/tmb/mpileup.yml";
-    //        //                break
-    //        case 'mutect2': varConfig = "$projectDir/assets/tmb/mutect2.yml";
-    //                        break
-    //        case 'strelka': varConfig = "$projectDir/assets/tmb/strelka.yml";
-    //                       break
-    //     }
+        String varConfig = "";
+
+        switch (variantcaller) {
+            case 'freebayes': varConfig = "/assets/tmb/freebayes.yml";
+                            break
+            case 'mutect2': varConfig = "/assets/tmb/mutect2.yml";
+                            break
+            case 'strelka': varConfig = "/assets/tmb/strelka.yml";
+                            break
+            // default:    log.warn "Please provide a valid variantcalling tool"
+            //             exit 1, "Unknown tool ${variantcaller}"
+        }
 
        return varConfig