Dsl2 multivcfanalyzer

assets/schema_fasta.json

@@ -137,6 +137,13 @@
                 "exists": true,
                 "errorMessage": "SNP annotation files for GATK must not contain any spaces and have file extension '.vcf'."
             }
+            "consensus_multivcfanalyzer_additional_vcf_files": {
+                "type": "string",
+                "format": "directory-path",
+                "pattern": "^\\S+$",
+                "exists": true,
+                "errorMessage": "The directory containing the additional vcf files for multivcfanalyzer must not contain any spaces and have file extensions ''."
+            }
         },
         "required": ["reference_name", "fasta"]
     }

conf/modules.config

@@ -1399,4 +1399,15 @@ process {
             pattern: '*.{glf,beagle}.gz'
         ]
     }
+
+    withName: MULTIVCFANALYZER {
+        tag = { "${meta.reference}" }
+        ext.prefix = { "multivcfanalyzer_${meta.reference}" }
+        publishDir = [
+            path: { "${params.outdir}/consensus_sequence/" },
+            mode: params.publish_dir_mode,
+            enabled: true,
+            pattern: '*.{fasta.gz,tsv,txt}'
+        ]
+    }
 }

modules.json

@@ -225,6 +225,11 @@
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     },
+                    "multivcfanalyzer": {
+                        "branch": "master",
+                        "git_sha": "b34fb117e397e72a070cde8adf21b758670c90f5",
+                        "installed_by": ["modules"]
+                    },
                     "picard/createsequencedictionary": {
                         "branch": "master",
                         "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",