From aeffe214c411a7d3bd38bd1fffaeed91e3792184 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 26 Jan 2024 11:27:34 +0000 Subject: [PATCH] Apply rnaseq -> riboseq fixes from code review Co-authored-by: Maxime U Garcia --- modules/local/gtf_filter/main.nf | 2 +- nextflow_schema.json | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/local/gtf_filter/main.nf b/modules/local/gtf_filter/main.nf index d14e8ff..b61d9cd 100644 --- a/modules/local/gtf_filter/main.nf +++ b/modules/local/gtf_filter/main.nf @@ -17,7 +17,7 @@ process GTF_FILTER { when: task.ext.when == null || task.ext.when - script: // filter_gtf.py is bundled with the pipeline, in nf-core/rnaseq/bin/ + script: // filter_gtf.py is bundled with the pipeline, in nf-core/riboseq/bin/ """ filter_gtf.py \\ --gtf $gtf \\ diff --git a/nextflow_schema.json b/nextflow_schema.json index f696c76..800ba5e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,8 +1,8 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/nf-core/rnaseq/master/nextflow_schema.json", - "title": "nf-core/rnaseq pipeline parameters", - "description": "RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.", + "$id": "https://raw.githubusercontent.com/nf-core/riboseq/master/nextflow_schema.json", + "title": "nf-core/riboseq pipeline parameters", + "description": "Analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting)", "type": "object", "definitions": { "input_output_options": { @@ -20,7 +20,7 @@ "pattern": "^\\S+\\.csv$", "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", - "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See [usage docs](https://nf-co.re/rnaseq/usage#samplesheet-input).", + "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/riboseq/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" }, "outdir": {