From 6d31a95117d086db86492827b243d38b4816a416 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 21 Oct 2026 20:42:45 +0200 Subject: [PATCH] Update nf-schema to 3.0.0 Migrate paramsHelp, paramsSummaryLog, and paramsSummaryMap to their single-options-map signatures; 3.0.0 requires Nextflow >= 26.04.0, matching our floor. Generated by OpenCode --- CHANGELOG.md | 1 + main.nf | 2 +- nextflow.config | 2 +- .../local/utils_nfcore_references_pipeline/main.nf | 7 +++---- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a1a478c..6cf6c392 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/main.nf b/main.nf index 8df4abc1..488b3968 100644 --- a/main.nf +++ b/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)], diff --git a/nextflow.config b/nextflow.config index 6c4b83fc..065725c5 100644 --- a/nextflow.config +++ b/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 diff --git a/subworkflows/local/utils_nfcore_references_pipeline/main.nf b/subworkflows/local/utils_nfcore_references_pipeline/main.nf index bdffc3f9..e9dac44b 100644 --- a/subworkflows/local/utils_nfcore_references_pipeline/main.nf +++ b/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() //