Added somatic cnvkit

CHANGELOG.md

@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#536](https://github.com/nf-core/sarek/pull/536) - Add `--step markduplicates` to start from duplicate marking, `--step prepare_recalibration` now ONLY starts at process `BaseRecalibrator` & adding `bam` and `cram` input support for `--step` `markduplicates`, `prepare_recalibration`, `recalibrate`, and `variant_calling`
 - [#538](https://github.com/nf-core/sarek/pull/538) - Add param `--seq_platform`, default: `ILLUMINA`
 - [#545](https://github.com/nf-core/sarek/pull/545) - Add modules and subworkflows for `cnvkit` tumor_only mode
+- [#540](https://github.com/nf-core/sarek/pull/540) - Add modules and subworkflows for `cnvkit` somatic mode
 
 ### Changed
 

conf/modules.config

@@ -735,6 +735,36 @@ process{
         ]
     }
 
+    //CNVKIT
+    withName: 'CNVKIT_ANTITARGET' {
+        ext.when         = { params.tools && params.tools.contains('cnvkit') }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/reference" },
+            pattern: "*{bed}"
+        ]
+    }
+
+    withName: 'CNVKIT_REFERENCE' {
+        ext.prefix       = "cnvkit"
+        ext.when         = { params.tools && params.tools.contains('cnvkit') }
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/reference" },
+            pattern: "*{cnn}"
+        ]
+    }
+
+    withName: 'CNVKIT_BATCH_TUMORONLY' {
+        ext.args         = { params.wes ? "--method hybrid --diagram --scatter" : "--method wgs --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,pdf,png}"
+        ]
+    }
+
     //MANTA
     withName: 'CONCAT_MANTA_TUMOR' {
         ext.prefix       = {"${meta.id}.tumor_sv"}
@@ -904,28 +934,8 @@ process{
             }
     }
 
-    // CNVKIT_TUMORONLY
-
-    withName: 'CNVKIT_ANTITARGET' {
-        ext.when         = { params.tools && params.tools.contains('cnvkit') }
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reference" },
-            pattern: "*{bed}"
-        ]
-    }
-
-    withName: 'CNVKIT_REFERENCE' {
-        ext.prefix       = "cnvkit"
-        ext.when         = { params.tools && params.tools.contains('cnvkit') }
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reference" },
-            pattern: "*{cnn}"
-        ]
-    }
-
-    withName: 'CNVKIT_BATCH_TUMORONLY' {
+    //CNVKIT
+    withName: 'CNVKIT_BATCH_SOMATIC' {
         ext.args         = { params.wes ? "--method hybrid --diagram --scatter" : "--method wgs --diagram --scatter" }
         ext.when         = { params.tools && params.tools.contains('cnvkit') }
         publishDir       = [
@@ -934,8 +944,6 @@ process{
             pattern: "*{bed,cnn,cnr,cns,pdf,png}"
         ]
     }
-
-
     //FREEBAYES
     withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_FREEBAYES_SOMATIC:FREEBAYES' {
         ext.args = "--pooled-continuous \

subworkflows/local/pair_variant_calling.nf

@@ -7,6 +7,7 @@ include { RUN_CONTROLFREEC_SOMATIC                  } from '../nf-core/variantca
 include { RUN_FREEBAYES as RUN_FREEBAYES_SOMATIC    } from '../nf-core/variantcalling/freebayes/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:
@@ -91,6 +92,17 @@ workflow PAIR_VARIANT_CALLING {
         ch_versions = ch_versions.mix(RUN_CONTROLFREEC_SOMATIC.out.versions)
     }
 
+    if (tools.contains('cnvkit')){
+        cram_pair_cnvkit = 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('freebayes')){
         RUN_FREEBAYES_SOMATIC(cram_pair_intervals, fasta, fasta_fai, intervals_bed_combine_gz)