Added somatic cnvkit

conf/modules.config

@@ -868,6 +868,17 @@ process{
             }
     }
 
+    //CNVKIT_BATCH
+    withName: 'CNVKIT_BATCH_SOMATIC' {
+        ext.args         = "--diagram --scatter"
+        ext.when         = { params.tools && params.tools.contains('cnvkit') }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/cnvkit" },
+            pattern: "*{bed,cnn,cnr,cns}"
+        ]
+    }
+
     //MANTA
     withName: 'CONCAT_MANTA_SOMATIC' {
         ext.prefix       = {"${meta.id}.somatic_sv"}

subworkflows/local/pair_variant_calling.nf

@@ -6,6 +6,7 @@ include { MSISENSORPRO_MSI_SOMATIC                  } from '../../modules/nf-cor
 include { RUN_CONTROLFREEC_SOMATIC                  } from '../nf-core/variantcalling/controlfreec/somatic/main.nf'
 include { RUN_MANTA_SOMATIC                         } from '../nf-core/variantcalling/manta/somatic/main.nf'
 include { RUN_STRELKA_SOMATIC                       } from '../nf-core/variantcalling/strelka/somatic/main.nf'
+include { RUN_CNVKIT_SOMATIC                        } from '../nf-core/variantcalling/cnvkit/somatic/main.nf'
 
 workflow PAIR_VARIANT_CALLING {
     take:
@@ -93,6 +94,17 @@ workflow PAIR_VARIANT_CALLING {
         ch_versions = ch_versions.mix(RUN_CONTROLFREEC_SOMATIC.out.versions)
     }
 
+    if (tools.contains('cnvkit')){
+        cram_test = cram_pair
+            .map{meta, normal_cram, normal_crai, tumor_cram, tumor_crai ->
+                [meta, tumor_cram, normal_cram]
+        }
+        RUN_CNVKIT_SOMATIC( cram_test,
+                            fasta,
+                            intervals_bed_combined,
+                            [])
+    }
+
     if (tools.contains('manta')) {
         RUN_MANTA_SOMATIC(  cram_pair_intervals_gz_tbi,
                             fasta,