some cleaning and making validParameters() work

main.nf

@@ -29,7 +29,7 @@ version = '2.0.0'
  * Input parameters:
 */
 
-params.resume          = false
+// params.resume          = false
 
 
 log_main = """
@@ -82,9 +82,7 @@ reclustered gene orthology file     : ${params.sub_orthologs}
 
 """
 
-include { paramsHelp; paramsSummaryMap; validateParameters } from 'plugin/nf-schema'
-
-if (params.resume) exit 1, "Are you making the classical --resume typo? Be careful!!!! ;)"
+include { paramsHelp; validateParameters } from 'plugin/nf-schema'
 
 // if( !workflow.resume ) {
 //     println "Removing the output folder"
@@ -101,11 +99,9 @@ include { SCORE } from "${LOCAL_SUBWORKFLOWS}/score.nf"
 
 include { PLOT } from "${WORKFLOWS}/plot.nf"
 
-// println paramsSummaryMap(workflow)
-
 workflow {
 
-    // validateParameters()
+    validateParameters()
 
     if (params.wf == "plot" ) {
         log.info(log_plot)

nextflow_schema.json

@@ -11,10 +11,6 @@
       "description": "",
       "default": "",
       "properties": {
-        "resume": {
-          "type": "string",
-          "description": "Convenient param for detecting resume mistake"
-        },
         "wf": {
           "type": "string",
           "description": "Workflow to be run, by default the main one. Alternative is plot",
@@ -35,13 +31,13 @@
         "annotations": {
           "type": "string",
           "description": "Path to GTF annotation files",
-          "format": "file-path",
+          "format": "file-path-pattern",
           "default": "./test/GTF/*_annot-subsetted.gtf.gz"
         },
         "genomes": {
           "type": "string",
           "description": "Path to fasta genome files",
-          "format": "file-path",
+          "format": "file-path-pattern",
           "default": "./test/GENOMES/*_gDNA-subsetted.fasta.gz"
         },
         "cluster": {
@@ -128,7 +124,7 @@
       }
     },
     "plot_parameters": {
-      "title": "Plot parameters",
+      "title": "Plot Parameters",
       "type": "object",
       "description": "Specific parameters for generating plots",
       "default": "",
@@ -161,7 +157,7 @@
         "output_plot": {
           "type": "string",
           "description": "Path where to store resulting plot",
-          "format": "file-path",
+          "format": "directory-path",
           "default": "./output_plot"
         }
       }
@@ -173,8 +169,7 @@
         "email": {
           "type": "string",
           "description": "Email for notification",
-          "format": "email",
-          "default": "[email protected]"
+          "format": "email"
         }
       }
     }

params.config.test

@@ -14,7 +14,7 @@ params {
     short_dist     = "2,0.50,0.60,0.25"
     prevaln        = null
     output         = "$projectDir/output_test"
-    email          = "[email protected]"
+    email          = null
     geneID         = "ENSG00000159055"
     output_plot    = "$projectDir/output_plot"
     relevant_exs   = "chr21:32274830-32274896"