Sarek bcftools normalization

conf/modules/post_variant_calling.config

@@ -16,6 +16,30 @@
 
 process {
 
+    withName: 'GERMLINE_VCFS_NORM'{
+        ext.args = { [
+            '--multiallelics - both', //split multiallelic sites into biallelic records and both SNPs and indels should be merged separately into two records
+            '--rm-dup all'            //output only the first instance of a record which is present multiple times
+        ].join(' ') }
+        ext.when   = { params.concatenate_vcfs }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/concat/${meta.id}/" }
+        ]
+    }
+
+        withName: 'VCFS_NORM'{
+        ext.args = { [
+            '--multiallelics - both', //split multiallelic sites into biallelic records and both SNPs and indels should be merged separately into two records
+            '--rm-dup all'            //output only the first instance of a record which is present multiple times
+        ].join(' ') }
+        ext.when   = { params.normalized_vcfs }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/normalized/${meta.id}/" }
+        ]
+    }
+
     withName: 'GERMLINE_VCFS_CONCAT'{
         ext.args   = { "-a" }
         ext.when   = { params.concatenate_vcfs }
@@ -34,11 +58,25 @@ process {
         ]
     }
 
+    withName: 'VCFS__SORT'{
+        ext.prefix = { "${meta.id}.norm" }
+        ext.when   = { params.normalized_vcfs }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/normalized/${meta.id}/" }
+        ]
+    }
+
     withName: 'TABIX_EXT_VCF' {
         ext.prefix = { "${input.baseName}" }
         ext.when   = { params.concatenate_vcfs }
     }
 
+    withName: 'TABIX_VCF' {
+        ext.prefix = { "${input.baseName}" }
+        ext.when   = { params.normalized_vcfs }
+    }
+
     withName: 'TABIX_GERMLINE_VCFS_CONCAT_SORT'{
         ext.prefix = { "${meta.id}.germline" }
         ext.when   = { params.concatenate_vcfs }
@@ -47,4 +85,13 @@ process {
                 path: { "${params.outdir}/variant_calling/concat/${meta.id}/" }
         ]
     }
+
+    withName: 'TABIX_VCFS_INDEX'{
+        ext.prefix = { "${meta.id}.norm" }
+        ext.when   = { params.normalized_vcfs }
+        publishDir = [
+            mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/norm/${meta.id}/" }
+        ]
+    }
 }

modules.json

@@ -26,6 +26,11 @@
                         "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
                         "installed_by": ["bam_ngscheckmate"]
                     },
+                    "bcftools/norm": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/sort": {
                         "branch": "master",
                         "git_sha": "487d92367b4d7bb9f1ca694bf72736be90720b15",