From 1e18f146899a99e3f80c17570322fdec92c07ff7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Fri, 20 Sep 2024 11:07:14 +0200 Subject: [PATCH 1/2] bump nf-schema to v2.1.1 in the template --- nf_core/pipeline-template/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index d129d1a49..16f57c94c 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -274,7 +274,7 @@ manifest { {% if nf_schema -%} // Nextflow plugins plugins { - id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { From e2c47405fba6c66609a982da928db6fa4d9a4b96 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Fri, 20 Sep 2024 13:08:30 +0200 Subject: [PATCH 2/2] remove help params from ignore params --- nf_core/pipeline-template/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 16f57c94c..3e301f0b0 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -278,7 +278,7 @@ plugins { } validation { - defaultIgnoreParams = ["genomes", "helpFull", "showHidden", "help-full", "show-hidden"] // The last 4 parameters are here because of a bug in nf-schema. This will be fixed in a later version + defaultIgnoreParams = ["genomes"] help { enabled = true command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir "