Merge pull request nf-core#113 from nf-core/fix-panel-file-validation

Fix validation issues after nf-core/tools v3 template update

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[PR #111](https://github.com/nf-core/pixelator/pull/111)] - Template update for nf-core/tools v3.0.2
 - [[PR #112](https://github.com/nf-core/pixelator/pull/112)] - Add graph refinement options for pixelator 0.19
+- [[PR #113](https://github.com/nf-core/pixelator/pull/113)] - Fix validation issues after nf-core/tools v3.0.2 update
 
 ### Parameters
 

nextflow_schema.json

@@ -26,7 +26,6 @@
                 "input_basedir": {
                     "type": "string",
                     "format": "directory-path",
-                    "exists": false,
                     "description": "Path to a local or remote directory that is the \"current working directory\" for relative paths defined in the input samplesheet",
                     "fa_icon": "fas fa-folder"
                 },

subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf

@@ -335,7 +335,7 @@ def resolve_relative_path(relative_path, URI samplesheet_path) {
 // Validate a given panel key if present against the (dynamic) set of panel options retrieved from pixelator
 //
 def validate_panel(LinkedHashMap meta, HashSet options) {
-    if (meta.panel == null) {
+    if (meta.panel == null || meta.panel == []) {
         return meta
     }
 
@@ -352,7 +352,7 @@ def validate_panel(LinkedHashMap meta, HashSet options) {
 // Validate a given design key if present against the (dynamic) set of design options retrieved from pixelator
 //
 def validate_design(LinkedHashMap meta, HashSet options) {
-    if (meta.design == null) {
+    if (meta.design == null || meta.design == []) {
         return meta
     }