Merge pull request #545 from SusiJo/cnv_tumor

Added cnvkit for tumor_only

Author: FriederikeHanssen

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#533](https://github.com/nf-core/sarek/pull/533) - Add param `--only_paired_variant_calling` to allow skipping of germline variantcalling for paired samples
 - [#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
 
 ### Changed
 
@@ -73,7 +74,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#513](https://github.com/nf-core/sarek/pull/513), [#527](https://github.com/nf-core/sarek/pull/527) - CNV is back
 - [#529](https://github.com/nf-core/sarek/pull/529) - Do not save `versions.yml` files
 - [#524](https://github.com/nf-core/sarek/pull/524) - Fix intervals usage by counting the actual list of scatter/gather files produced and not overall number of intervals
-- [#549](https://github.com/nf-core/sarek/pull/549) - Fix unique lanes required for Freebayes: issue [#311](https://github.com/nf-core/sarek/issues/311), replaces `meta.clone()` with actual copy of map to avoid issues with https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339
+- [#549](https://github.com/nf-core/sarek/pull/549) - Fix unique lanes required for Freebayes: issue [#311](https://github.com/nf-core/sarek/issues/311), replaces `meta.clone()` with actual copy of map to avoid issues with <https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339>
 
 ### Deprecated
 

conf/modules.config

@@ -904,6 +904,38 @@ 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' {
+        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}"
+        ]
+    }
+
+
     //FREEBAYES
     withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_FREEBAYES_SOMATIC:FREEBAYES' {
         ext.args = "--pooled-continuous \

modules.json

@@ -30,8 +30,14 @@
             "cat/fastq": {
                 "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
             },
+            "cnvkit/antitarget": {
+                "git_sha": "58c5ec2f4eb44eff1fb7cc9e02df07bd448c6aaf"
+            },
             "cnvkit/batch": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "9096be5464d800156761b7c73c574f5a5bad2f72"
+            },
+            "cnvkit/reference": {
+                "git_sha": "8208140d21f3a754fff2e177db7a0e570fa2af6e"
             },
             "controlfreec/assesssignificance": {
                 "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b"