Merge pull request #704 from FriederikeHanssen/fix_schema

freec ploidy number -> String

Author: FriederikeHanssen

CHANGELOG.md

@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#681](https://github.com/nf-core/sarek/pull/681) - Fixed intermediate files published cf [#680](https://github.com/nf-core/sarek/issues/680)
 - [#688](https://github.com/nf-core/sarek/pull/688) - Fixed VEP plugins issue cf [#687](https://github.com/nf-core/sarek/issues/687)
 - [#689](https://github.com/nf-core/sarek/pull/689) - Fixed when clause for non `BWA mem` building mapping indexes
+- [#704](https://github.com/nf-core/sarek/pull/704) - Fixed `cf_ploidy` to string instead of number
 
 ### Deprecated
 

nextflow.config

@@ -55,7 +55,7 @@ params {
     ascat_min_counts = 10               // default value for ASCAT
     ascat_min_map_qual = 35             // default value for ASCAT
     ascat_purity = null                 // default value for ASCAT
-    cf_ploidy = 2                       // default value for Control-FREEC
+    cf_ploidy = "2"                     // default value for Control-FREEC
     cf_coeff = 0.05                     // default value for Control-FREEC
     cf_contamination = 0                // default value for Control-FREEC
     cf_contamination_adjustment = false // by default we are not using this in Control-FREEC
@@ -101,7 +101,7 @@ params {
     help                       = false
     validate_params            = true
     show_hidden_params         = false
-    schema_ignore_params       = 'genomes,snpeff_version,vep_version'
+    schema_ignore_params       = 'genomes,snpeff_version,vep_version,cf_ploidy'
     enable_conda               = false
 
     // Config options

nextflow_schema.json

@@ -316,8 +316,8 @@
                     "help_text": "Details, see [ControlFREEC manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html)."
                 },
                 "cf_ploidy": {
-                    "type": "integer",
-                    "default": 2,
+                    "type": "string",
+                    "default": "2",
                     "fa_icon": "fas fa-bacon",
                     "help_text": "In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs Example: ploidy=2 , ploidy=2,3,4. For more details, see the [manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html).",
                     "description": "Genome ploidy used by ControlFREEC",