Add cnvkit germline mode

CHANGELOG.md

@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#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
+- [#573](https://github.com/nf-core/sarek/pull/573) - Add modules and subworkflows for `cnvkit` germline mode
 
 ### Changed
 

conf/modules.config

@@ -483,6 +483,17 @@ process{
         ]
     }
 
+    // CNVKIT_GERMLINE
+    withName: 'CNVKIT_BATCH_GERMLINE' {
+        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}"
+        ]
+    }
+
     // DEEPVARIANT
     withName: 'CONCAT_DEEPVARIANT_.*' {
         publishDir       = [

subworkflows/local/germline_variant_calling.nf

@@ -7,6 +7,7 @@ include { RUN_FREEBAYES       } from '../nf-core/variantcalling/freebayes/main.n
 include { RUN_HAPLOTYPECALLER } from '../nf-core/variantcalling/haplotypecaller/main.nf'
 include { RUN_MANTA_GERMLINE  } from '../nf-core/variantcalling/manta/germline/main.nf'
 include { RUN_STRELKA_SINGLE  } from '../nf-core/variantcalling/strelka/single/main.nf'
+include { RUN_CNVKIT_GERMLINE  } from '../nf-core/variantcalling/cnvkit/germline/main.nf'
 //include { TIDDIT          } from './variantcalling/tiddit.nf'
 
 workflow GERMLINE_VARIANT_CALLING {
@@ -21,6 +22,7 @@ workflow GERMLINE_VARIANT_CALLING {
         intervals_bed_gz_tbi         // channel: [mandatory] intervals/target regions index zipped and indexed
         intervals_bed_combine_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed in one file
         intervals_bed_combine_gz     // channel: [mandatory] intervals/target regions index zipped in one file
+        intervals_bed_combined       // channel: [mandatory] intervals/target regions in one file unzipped
         // joint_germline               // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment
 
     main:
@@ -62,6 +64,24 @@ workflow GERMLINE_VARIANT_CALLING {
             cram, crai, bed_new, tbi_new]
         }
 
+    // CNVKIT
+    cram_recalibrated.view()
+
+    if(params.tools.contains('cnvkit')){
+        cram_recalibrated_cnvkit = cram_recalibrated
+            .map{ meta, cram, crai ->
+                [meta, [], cram]
+            }
+
+        cram_recalibrated_cnvkit.view()
+
+        RUN_CNVKIT_GERMLINE(cram_recalibrated_cnvkit,
+                            fasta,
+                            intervals_bed_combined,
+                            [])
+        ch_versions     = ch_versions.mix(RUN_CNVKIT_GERMLINE.out.versions)
+    }
+
     // DEEPVARIANT
     if(params.tools.contains('deepvariant')){
         RUN_DEEPVARIANT(cram_recalibrated_intervals, fasta, fasta_fai, intervals_bed_combine_gz)

workflows/sarek.nf

@@ -781,7 +781,8 @@ workflow SAREK {
             intervals,
             intervals_bed_gz_tbi,
             intervals_bed_combined_gz_tbi,
-            intervals_bed_combined_gz)
+            intervals_bed_combined_gz,
+            intervals_bed_combined)
             // params.joint_germline)
 
         // TUMOR ONLY VARIANT CALLING