intialise varloc calls sw

modules.json

@@ -451,6 +451,21 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "varlociraptor/callvariants": {
+                        "branch": "master",
+                        "git_sha": "99b332c63d7a6dbef648a2a2c2b03f997ca8e5d1",
+                        "installed_by": ["modules"]
+                    },
+                    "varlociraptor/estimatealignmentproperties": {
+                        "branch": "master",
+                        "git_sha": "99b332c63d7a6dbef648a2a2c2b03f997ca8e5d1",
+                        "installed_by": ["modules"]
+                    },
+                    "varlociraptor/preprocess": {
+                        "branch": "master",
+                        "git_sha": "99b332c63d7a6dbef648a2a2c2b03f997ca8e5d1",
+                        "installed_by": ["modules"]
+                    },
                     "vcftools": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

subworkflows/local/post_variantcalling/main.nf

@@ -3,10 +3,14 @@
 //
 
 include { CONCATENATE_GERMLINE_VCFS } from '../vcf_concatenate_germline/main'
+include { VARLOCIRAPTOR_CALLS       } from '../vcf_varlociraptor_calls/main'
 
 workflow POST_VARIANTCALLING {
 
     take:
+    cram
+    fasta
+    fasta_fai
     vcfs
     concatenate_vcfs
 
@@ -20,6 +24,9 @@ workflow POST_VARIANTCALLING {
         versions = versions.mix(CONCATENATE_GERMLINE_VCFS.out.versions)
     }
 
+    VARLOCIRAPTOR_CALLS(cram, fasta, fasta_fai)
+    versions = versions.mix(VARLOCIRAPTOR_CALLS.out.versions)
+
     emit:
     vcfs // post processed vcfs