Merge pull request #607 from nf-core/smallfix

Change platform description and update vcf2cytosure conditional
nf-core · Sep 11, 2024 · 36a957e · 36a957e
2 parents d513968 + 68133d6
commit 36a957e
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -485,9 +485,9 @@
                 "analysis_type": {
                     "type": "string",
                     "default": "wgs",
-                    "description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
+                    "description": "Specifies which analysis type for the pipeline- either 'wgs' or 'wes'. This changes resources consumed and tools used.",
                     "fa_icon": "fas fa-align-center",
-                    "enum": ["wgs", "wes", "mito"]
+                    "enum": ["wgs", "wes"]
                 },
                 "bwa_as_fallback": {
                     "type": "boolean",
@@ -498,9 +498,8 @@
                 "platform": {
                     "type": "string",
                     "default": "illumina",
-                    "description": "Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.",
-                    "fa_icon": "fas fa-align-center",
-                    "enum": ["illumina"]
+                    "description": "Specifies the platform on which the reads were sequenced.",
+                    "fa_icon": "fas fa-align-center"
                 },
                 "ngsbits_samplegender_method": {
                     "type": "string",

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -785,7 +785,7 @@ workflow RAREDISEASE {
     Generate CGH files from sequencing data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-    if ( !params.skip_vcf2cytosure && params.analysis_type.equals("wgs") && !params.skip_sv_calling) {
+    if ( !params.skip_vcf2cytosure && params.analysis_type.equals("wgs") && !params.skip_sv_calling && !params.skip_sv_annotation) {
         GENERATE_CYTOSURE_FILES (
             ch_sv_annotate.vcf_ann,
             ch_sv_annotate.tbi,