please be fixed2

nf-core · Jul 3, 2023 · e18260c · e18260c
1 parent ed16042
commit e18260c
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Showing 3 changed files with 17 additions and 26 deletions.
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
@@ -20,31 +20,6 @@ class WorkflowMain {
             "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
     }
 
-    //
-    // Generate help string
-    //
-    public static String help(workflow, params, log) {
-        def command = "nextflow run ${workflow.manifest.name} --input sequences.fasta -profile docker"
-        def help_string = ''
-        help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
-        help_string += NfcoreSchema.paramsHelp(workflow, params, command)
-        help_string += '\n' + citation(workflow) + '\n'
-        help_string += NfcoreTemplate.dashedLine(params.monochrome_logs)
-        return help_string
-    }
-
-    //
-    // Generate parameter summary log string
-    //
-    public static String paramsSummaryLog(workflow, params) {
-        def summary_log = ''
-        summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
-        summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
-        summary_log += '\n' + citation(workflow) + '\n'
-        summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
-        return summary_log
-    }
-
     //
     // Validate parameters and print summary to screen
     //

diff --git a/nextflow.config b/nextflow.config
@@ -269,7 +269,7 @@ manifest {
     homePage        = 'https://github.com/nf-core/pangenome'
     description     = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=22.10.1'
+    nextflowVersion = '!>=23.04.0'
     version         = '1.0.0'
     doi             = ''
 }

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -464,6 +464,22 @@
                     "default": false,
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                },
+                "show_hidden_params": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Do we want to display hidden parameters?",
+                    "default": false,
+                    "hidden": true,
+                    "help_text": "Do we want to display hidden parameters?"
+                },
+                "schema_ignore_params": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Do we want to display hidden parameters?",
+                    "default": "igenomes_base",
+                    "hidden": true,
+                    "help_text": "Do we want to display hidden parameters?"
                 }
             }
         }