From 1279437aa105f8fdf5feb73f57ccf66aa06b1702 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 20 Dec 2022 21:48:08 +0100 Subject: [PATCH] Apply suggestions from code review --- nextflow.config | 2 +- nextflow_schema.json | 9 --------- 2 files changed, 1 insertion(+), 10 deletions(-) diff --git a/nextflow.config b/nextflow.config index acfe2a0..f5ab538 100644 --- a/nextflow.config +++ b/nextflow.config @@ -38,7 +38,7 @@ params { version = false validate_params = true show_hidden_params = false - schema_ignore_params = 'genomes' + schema_ignore_params = 'genomes,fasta' // Config options diff --git a/nextflow_schema.json b/nextflow_schema.json index 6d48671..0c7ce3d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -712,15 +712,6 @@ "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.", "hidden": true }, - "fasta": { - "type": "string", - "description": "Path to FASTA genome file.", - "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", - "pattern": "^\\\\S+\\\\.fn?a(sta)?(\\\\.gz)?$", - "format": "file-path", - "mimetype": "text/plain", - "fa_icon": "far fa-file-code" - }, "igenomes_base": { "type": "string", "format": "directory-path",