v1.0.0 fixes (#380)

* fix syntax of optional

- fix ambiguity in features list definition

* remove optional input definition

Author: FerriolCalvet

docs/file_formatting.md

@@ -96,7 +96,7 @@ params {
     features_table              = "features_example.csv"
     features_table_separator    = 'comma'
     features_unique_identifier  = 'SAMPLE_ID'
-    features_groups_list        = [ ["BLADDER_LOCATION"], ["BLADDER_LOCATION", "SEX"], ["BLADDER_LOCATION", "SEX", "SMOKING_STATUS"] ]
+    features_groups_list        = "[ ["BLADDER_LOCATION"], ["BLADDER_LOCATION", "SEX"], ["BLADDER_LOCATION", "SEX", "SMOKING_STATUS"] ]"
 }
 ```
 

modules/local/expand_regions/main.nf

@@ -7,9 +7,9 @@ process EXPAND_REGIONS {
 
     input:
     tuple val(meta), path(panel)
-    path (domains, optional: true)
-    path (exons, optional: true)
-    path (custom, optional: true)
+    path (domains)
+    path (exons)
+    path (custom)
 
     output:
     tuple val(meta), path("*with_hotspots.tsv") , emit: panel_increased