update trait_efo -> efo_id

PGScatalog · Jul 31, 2024 · ce4d596 · ce4d596
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diff --git a/docs/getting-started.rst b/docs/getting-started.rst
@@ -98,7 +98,7 @@ parameter:
     --pgs_id PGS001229 # one score
     --pgs_id PGS001229,PGS001405 # many scores separated by , (no spaces)
 
-.. note:: You can also select scores associated with traits (``--trait_efo``) and
+.. note:: You can also select scores associated with traits (``--efo_id``) and
           publications (``--pgp_id``)
 
 If you would like to use a custom scoring file not published in the PGS Catalog,

diff --git a/docs/how-to/calculate_pgscatalog.rst b/docs/how-to/calculate_pgscatalog.rst
@@ -46,12 +46,12 @@ Traits
 ~~~~~~
 
 If you would like to calculate every polygenic score in the Catalog for a
-`trait`_, like `coronary artery disease`_, then you can use the ``--trait_efo``
+`trait`_, like `coronary artery disease`_, then you can use the ``--efo_id``
 parameter:
 
 .. code-block:: console
 
-    --trait_efo EFO_0001645
+    --efi_id EFO_0001645
 
 Multiple traits can be set by using a comma separated list.
 
@@ -85,7 +85,7 @@ Multiple traits can be set by using a comma separated list.
         -profile <docker/singularity/conda> \    
         --input samplesheet.csv \
         --pgs_id PGS001229 \
-        --trait_efo EFO_0001645 \
+        --efo_id EFO_0001645 \
         --pgp_id PGP000001
 
 .. note:: For more details about calculating multiple scores, see :ref:`multiple`