Update nf-schema to 3.0.0

CHANGELOG.md

@@ -66,6 +66,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#161](https://github.com/nf-core/references/pull/161) - Document `references_base_path` description and igenomes prefix-rewriting behaviour
 - [#161](https://github.com/nf-core/references/pull/161) - Replace placeholder `TODO` error messages in `schema_references.json`
 - [#162](https://github.com/nf-core/references/pull/162) - Resolve datasheet `splice_sites` paths to files so publishing works on Nextflow 26.10
+- [#163](https://github.com/nf-core/references/pull/163) - Update nf-schema to 3.0.0 and migrate `paramsHelp`, `paramsSummaryLog`, and `paramsSummaryMap` to their single-options-map signatures
 - [#162](https://github.com/nf-core/references/pull/162) - Merge `prepare_genome_dnaseq` and `prepare_genome_rnaseq` into a single `prepare_genome` subworkflow
 
 ### Removed

main.nf

@@ -314,7 +314,7 @@ workflow {
     multiqc_files = channel.empty()
     multiqc_report = channel.empty()
 
-    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    summary_params = paramsSummaryMap(parameters_schema: "nextflow_schema.json")
     workflow_summary = record(
         name: 'workflow_summary_mqc.yaml',
         items: [paramsSummaryMultiqc(summary_params)],

nextflow.config

@@ -249,7 +249,7 @@ manifest {
 // Nextflow plugins
 plugins {
     id 'nf-core-utils@0.4.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
-    id 'nf-schema@2.7.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@3.0.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 // enable lineage

subworkflows/local/utils_nfcore_references_pipeline/main.nf

@@ -104,8 +104,7 @@ workflow PIPELINE_INITIALISATION {
         }
         log.info(
             paramsHelp(
-                help_options,
-                help instanceof String ? help : "",
+                help_options + [parameter: help instanceof String ? help : ""],
             )
         )
         exit(0)
@@ -121,7 +120,7 @@ workflow PIPELINE_INITIALISATION {
         summary_options << [parametersSchema: null]
     }
     log.info(before_text)
-    log.info(paramsSummaryLog(summary_options, workflow))
+    log.info(paramsSummaryLog(summary_options))
     log.info(after_text)
 
     extra_text = """
@@ -184,7 +183,7 @@ workflow PIPELINE_COMPLETION {
     multiqc_report //  string: Path to MultiQC report
 
     main:
-    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    summary_params = paramsSummaryMap(parameters_schema: "nextflow_schema.json")
     def multiqc_reports = multiqc_report.toList()
 
     //