diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 1bfc45c..d125f40 100755 --- 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 index fbab4a9..17f52e2 100644 --- 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 index 352bd1f..44f6c3f 100644 --- 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?" } } }