Merge pull request #1471 from maxulysse/schema

fix(schema): add some params to validationSchemaIgnoreParams for better handling

Author: maxulysse

CHANGELOG.md

@@ -59,6 +59,9 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
 - [#1463](https://github.com/nf-core/sarek/pull/1463) - Add `spark` profile to all gatk4spark tests
 - [#1465](https://github.com/nf-core/sarek/pull/1465), [#1469](https://github.com/nf-core/sarek/pull/1469) - Fix input channels and tests of Sentieon workflows
 - [#1470](https://github.com/nf-core/sarek/pull/1470) - Fix channels for `MultiQC`
+- [#1471](https://github.com/nf-core/sarek/pull/1471) - Add `snpeff_db` params to `validationSchemaIgnoreParams` to fix issues with Seqera Platform
+- [#1471](https://github.com/nf-core/sarek/pull/1471) - Add `vep_cache_version` params to `validationSchemaIgnoreParams` to fix [#1454](https://github.com/nf-core/sarek/issues/1454)
+- [#1471](https://github.com/nf-core/sarek/pull/1471) - Update `vep_version` params match the actual tool version
 
 ### Removed
 

nextflow.config

@@ -97,7 +97,7 @@ params {
     vep_out_format           = "vcf"
     vep_spliceai             = null // spliceai plugin disabled within VEP
     vep_spliceregion         = null // spliceregion plugin disabled within VEP
-    vep_version              = "110.0-0"      // Should be updated when we update VEP, needs this to get full path to some plugins
+    vep_version              = "111.0-0"      // Should be updated when we update VEP, needs this to get full path to some plugins
 
     // MultiQC options
     multiqc_config             = null
@@ -136,7 +136,7 @@ params {
     // Schema validation default options
     validationFailUnrecognisedParams = false
     validationLenientMode            = true
-    validationSchemaIgnoreParams     = 'cf_ploidy,genomes,igenomes_base'
+    validationSchemaIgnoreParams     = 'cf_ploidy,snpeff_db,vep_cache_version,genomes,igenomes_base'
     validationShowHiddenParams       = false
     validate_params                  = true
 }

nextflow_schema.json

@@ -520,7 +520,7 @@
                 },
                 "vep_version": {
                     "type": "string",
-                    "default": "110.0-0",
+                    "default": "111.0-0",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Should reflect the VEP version used in the container.",
                     "help_text": "Used by the loftee plugin that need the full path."
@@ -785,7 +785,7 @@
                     "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nAlternatively species listed in Ensembl Genomes caches can be used."
                 },
                 "vep_cache_version": {
-                    "type": "number",
+                    "type": "string",
                     "fa_icon": "fas fa-tag",
                     "description": "VEP cache version.",
                     "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nAlternatively cache version can be use to specify the correct Ensembl Genomes version number as these differ from the concurrent Ensembl/VEP version numbers"