Make vcf generation optional

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local module: `ENSEMBL_DOWNLOAD` [#539](https://github.com/nf-core/rnafusion/pull/539)
 - Add nf-test to local module: `HGNC_DOWNLOAD` [#540](https://github.com/nf-core/rnafusion/pull/540)
 - Add nf-test to nf-core module: `PICARD_COLLECTRNASEQMETRICS` and update module [#551](https://github.com/nf-core/rnafusion/pull/551)
+- Add `--skip_vcf` boolean parameter to skip vcf file generation [#554](https://github.com/nf-core/rnafusion/pull/554)
 
 ### Changed
 

conf/modules.config

@@ -354,6 +354,6 @@ process {
     }
 
     withName: 'VCF_COLLECT' {
-        ext.when = {!params.fusioninspector_only}
+        ext.when = { {!params.fusioninspector_only} && {!params.skip_vcf} }
     }
 }

nextflow.config

@@ -71,6 +71,7 @@ params {
     // Skip steps
     skip_qc                    = false
     skip_vis                   = false
+    skip_vcf                   = false
 
     // Path to references
     ensembl_ref                   = "${params.genomes_base}/ensembl"

nextflow_schema.json

@@ -18,6 +18,10 @@
                 "skip_vis": {
                     "type": "boolean",
                     "description": "Skip visualisation steps"
+                },
+                "skip_vcf": {
+                    "type": "boolean",
+                    "description": "Skip vcf generation step"
                 }
             },
             "fa_icon": "fas fa-fast-forward"