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update annotations link in rnaseq workflow doc #192

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bnovak32 merged 1 commit into from
Feb 11, 2026
Merged

update annotations link in rnaseq workflow doc #192

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4 changes: 2 additions & 2 deletions RNAseq/Workflow_Documentation/NF_RCP/README.md
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Expand Up @@ -225,7 +225,7 @@ nextflow run NF_RCP_2.0.1/main.nf \
--reference_fasta <url/or/path/to/fasta> \
--reference_gtf <url/or/path/to/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.

Expand Down Expand Up @@ -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`
Expand Down
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