module import for addreadgroups

Author: ilight1542

conf/modules.config

@@ -1585,6 +1585,23 @@ process {
     //
     // GENOTYPING
     //
+    withName: PICARD_ADDORREPLACEREADGROUPS {
+        tag = { "${meta.reference}|${meta.library_id}" }
+        ext.args ={
+            se_pe_string = meta.single_end ? "SE" : "PE"
+            [
+                "--RGID ILLUMINA-${meta.library_id}",
+                "--RGSM ${meta.library_id}",
+                "--RGLB ${meta.library_id}",
+                "--RGPL illumina",
+                "--RGPU ILLUMINA-${meta.sample_id}_${meta.library_id}-${meta.strandedness}_stranded-${se_pe_string}"
+            ].join(' ').trim() }
+        ext.prefix = { "${meta.sample_id}_${meta.library_id}_${meta.reference}_unique_rgid" }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
     withName: SAMTOOLS_MPILEUP_PILEUPCALLER {
         tag = { "${meta.reference}|${meta.strandedness}" }
         ext.args = [

modules.json

@@ -225,6 +225,11 @@
                         "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     },
+                    "picard/addorreplacereadgroups": {
+                        "branch": "master",
+                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "installed_by": ["modules"]
+                    },
                     "picard/createsequencedictionary": {
                         "branch": "master",
                         "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",