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EBIvariation · Dec 11, 2023 · 598645f · 598645f
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diff --git a/README.md b/README.md
@@ -73,6 +73,7 @@ nextflow run ${CODE_ROOT}/pipelines/annotation_pipeline.nf \
   --mappings ${LATEST_MAPPINGS} \
   -resume
 ```
+You can use the `--include_transcripts` flag to also include transcript annotations with the functional consequences.
 
 By default, the pipeline will download and annotate the latest ClinVar XML dump from [FTP](https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/). If you want to run it on an existing XML file, you can pass it via the `--clinvar` flag.
 

diff --git a/cmat/consequence_prediction/repeat_expansion_variants/pipeline.py b/cmat/consequence_prediction/repeat_expansion_variants/pipeline.py
@@ -249,7 +249,7 @@ def main(clinvar_xml, include_transcripts, output_consequences=None, output_data
 
     Args:
         clinvar_xml: filepath to the ClinVar XML file.
-        include_transcripts:
+        include_transcripts: whether to include transcript IDs along with consequence terms.
         output_consequences: filepath to the output file with variant consequences. The file uses a 6-column format
             compatible with the VEP mapping pipeline (see /consequence_prediction/README.md).
         output_dataframe: filepath to the output file with the full dataframe used in the analysis. This will contain