From 3c22fe9b5878c480f73b3fc13f1b5c76c0427b1f Mon Sep 17 00:00:00 2001 From: Alexis Torres Date: Wed, 11 Feb 2026 09:05:00 -0800 Subject: [PATCH] update annotations link in rnaseq workflow doc --- RNAseq/Workflow_Documentation/NF_RCP/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RNAseq/Workflow_Documentation/NF_RCP/README.md b/RNAseq/Workflow_Documentation/NF_RCP/README.md index 81df0ea5..19a3ac34 100644 --- a/RNAseq/Workflow_Documentation/NF_RCP/README.md +++ b/RNAseq/Workflow_Documentation/NF_RCP/README.md @@ -225,7 +225,7 @@ nextflow run NF_RCP_2.0.1/main.nf \ --reference_fasta \ --reference_gtf ``` -> Note: This approach should be used for organisms not listed in the [GeneLab annotations table](https://github.com/nasa/GeneLab_Data_Processing/blob/master/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110_annotations.csv). +> Note: This approach should be used for organisms not listed in the [GeneLab annotations table](https://github.com/nasa/GeneLab_Data_Processing/blob/master/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv). > Note: The `--reference_source` and `--reference_version` parameters should match the reference source and version number of the reference fasta and gtf files used. @@ -286,7 +286,7 @@ nextflow run NF_RCP_2.0.1/main.nf \ * `--gene_annotations_file` - Specifies the URL or path to a gene annotation file that adds additional gene annotation columns to the differential expression output table. This can be: - - The file listed in the `genelab_annots_link` column of the [GeneLab annotations table](https://github.com/nasa/GeneLab_Data_Processing/blob/master/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110/GL-DPPD-7110_annotations.csv) + - The file listed in the `genelab_annots_link` column of the [GeneLab annotations table](https://github.com/nasa/GeneLab_Data_Processing/blob/master/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv) - A custom gene annotation file where: - For organisms listed in the GeneLab annotations table: gene IDs must be in a column with the same name as column 1 of the GeneLab organism-specific gene annotation file - For organisms not listed in the table: gene IDs must be in a column named `gene_id`