minor fixes on schemawith the workflow

main.nf

@@ -11,13 +11,13 @@ def logo() {
     c_cyan = "\033[0;36m";
     c_white = "\033[0;37m";
 
-    return """    ${c_dim}----------------------------------------------------${c_reset}${c_green}
-       ____  __  ______
-      / __ \\/  |/  /   |
-     / / / / /|_/ / /| |
-    / /_/ / /  / / ___ |
-    \\____/_/  /_/_/  |_|
-    ${c_reset}${c_dim}----------------------------------------------------${c_reset}""".stripIndent()
+    return """    ${c_dim}------------------------------------------------------------------------------${c_reset}${c_green}
+       ____  __  ______       ____                                       ____        _ __    __
+      / __ \/  |/  /   |     / __ )_________ _      __________  _____   / __ )__  __(_) /___/ /
+     / / / / /|_/ / /| |    / __  / ___/ __ \ | /| / / ___/ _ \/ ___/  / __  / / / / / / __  /
+    / /_/ / /  / / ___ |   / /_/ / /  / /_/ / |/ |/ (__  )  __/ /     / /_/ / /_/ / / / /_/ /
+    \____/_/  /_/_/  |_|  /_____/_/   \____/|__/|__/____/\___/_/     /_____/\__,_/_/_/\__,_/
+    ${c_reset}${c_dim}------------------------------------------------------------------------------${c_reset}""".stripIndent()
 }
 
 // Print the logo
@@ -26,11 +26,11 @@ log.info logo()
 // Load Plugins
 include { validateParameters; paramsHelp; paramsSummaryLog } from 'plugin/nf-schema'
 
-    // Print help message if needed
-    if (params.help){
-        log.info paramsHelp("nextflow run main.nf required [optional]")
-        exit 0
-    }
+// Print help message if needed
+if (params.help){
+    log.info paramsHelp("nextflow run main.nf required [optional]")
+    exit 0
+}
 
 // Validate input parameters
 validateParameters()
@@ -63,19 +63,21 @@ output {
             { file -> "data/OmaServer.h5" }
         }
     }
+
+    'data' { mode 'copy'}
 }
 
 workflow {
     OMA_browser_build()
-}
 
-workflow.onComplete {
-    println "Pipeline completed at: ${workflow.complete}"
-    println "Time to complete workflow execution: ${workflow.duration}"
-    println "Execution status: ${workflow.success ? 'Successful' : 'Failed'}"
-    println "Reports stored in ${params.outputDir}/reports/nextflow"
-}
+    workflow.onComplete {
+        println "Pipeline completed at: ${workflow.complete}"
+        println "Time to complete workflow execution: ${workflow.duration}"
+        println "Execution status: ${workflow.success ? 'Successful' : 'Failed'}"
+        println "Reports stored in ${params.outputDir}/reports/nextflow"
+    }
 
-workflow.onError {
-    println "Error... Pipeline execution stopped with the following message: $workflow.errorMessage"
-}
+    workflow.onError {
+        println "Error... Pipeline execution stopped with the following message: $workflow.errorMessage"
+    }
+}

nextflow.config

@@ -1,6 +1,6 @@
 // Nextflow configuration
 nextflow.enable.moduleBinaries = true // Enables the use of modules with binary scripts
-
+nextflow.preview.output = true        // Enables publish/output section for workflows
 
 // Global default params
 params {

nextflow_schema.json

@@ -1,26 +1,10 @@
 {
-  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "$schema": "http://json-schema.org/draft-07/schema",
   "$id": "https://raw.githubusercontent.com/oma-browser-build/master/nextflow_schema.json",
   "title": "oma-browser-build pipeline parameters",
   "description": "Convert OMA run into OMA Browser release",
   "type": "object",
-  "defs": {
-    "input_output_options": {
-      "title": "Input/output options",
-      "type": "object",
-      "fa_icon": "fas fa-terminal",
-      "description": "Define where the pipeline should find input data and save output data.",
-      "required": ["outdir"],
-      "properties": {
-        "outdir": {
-          "type": "string",
-          "format": "directory-path",
-          "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
-          "fa_icon": "fas fa-folder-open",
-          "default": "./results"
-        }
-      }
-    },
+  "definitions": {
     "generic_options": {
       "title": "Generic options",
       "type": "object",
@@ -39,27 +23,63 @@
   },
   "allOf": [
     {
-      "$ref": "#/defs/input_output_options"
-    },
-    {
-      "$ref": "#/defs/generic_options"
+      "$ref": "#/definitions/generic_options"
     }
   ],
   "properties": {
-    "orthoxml": {
+    "hog_orthoxml": {
       "type": "string"
     },
-    "genomes": {
+    "matrix_file": {
       "type": "string"
     },
+    "pairwise_orthologs_folder": {
+      "type": "string"
+    },
+    "genomes_dir": {
+      "type": "string"
+    },
+    "known_domains": {
+      "type": "string"
+    },
+    "cath_names_path": {
+      "type": "string",
+      "default": "http://download.cathdb.info/cath/releases/latest-release/cath-classification-data/cath-names.txt"
+    },
+    "pfam_names_path": {
+      "type": "string",
+      "default": "https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz"
+    },
+    "xref_uniprot_swissprot": {
+      "type": "string",
+      "default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz"
+    },
+    "xref_uniprot_trembl": {
+      "type": "string",
+      "default": "/dev/null"
+    },
+    "xref_refseq": {
+      "type": "string"
+    },
+    "go_obo": {
+      "type": "string",
+      "default": "http://purl.obolibrary.org/obo/go/go-basic.obo"
+    },
+    "go_gaf": {
+      "type": "string",
+      "default": "https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz"
+    },
     "oma_browser_data_dir": {
       "type": "string",
-      "format": "directory-path",
       "default": "test/bla"
     },
     "nr_medium_procs": {
       "type": "integer",
       "default": 10
+    },
+    "outputDir": {
+      "type": "string",
+      "default": "./results"
     }
   }
 }