Added better worfklow run description when using --help

nf-core · Jan 30, 2024 · 04b9d30 · 04b9d30
1 parent 7373cbe
commit 04b9d30
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/main.nf b/main.nf
@@ -33,7 +33,7 @@ include { validateParameters; paramsHelp } from 'plugin/nf-validation'
 if (params.help) {
     def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
     def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh38 -profile docker -outdir results --circle_identifier [circexplorer2,circle_map_realign,circle_map_repeats,circle_finder,unicycler,ampliconarchitect]"
     log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
     System.exit(0)
 }

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -70,7 +70,7 @@
             "properties": {
                 "circle_identifier": {
                     "type": "string",
-                    "description": "Specifies the circular DNA identification algorithm to use - available 'circle_map_realign', 'circle_map_repeats', 'circle_finder', 'circexplorer2', and 'ampliconarchitect'.",
+                    "description": "Specifies the circular DNA identification algorithm to use - available 'circle_map_realign', 'circle_map_repeats', 'circle_finder', 'circexplorer2', and 'ampliconarchitect'. Multiple circle_identifier's can be specified with a comma-separated string. E.g. `--circle_identifier 'circle_map_realign,unicycler'`.",
                     "help_text": "Specify the circle_identifier branch used. Multiple circle_identifier's can be specified with a comma-separated string. E.g. `--circle_identifier 'circle_map_realign,unicycler'`.",
                     "fa_icon": "fas fa-circle-notch",
                     "default": "circle_map_realign"