Update `min_length` section in workflow config ref
Add a note that the `min_length` filter is applied to masked sequences.
Users have been confused why their sequences fail the filter when they
only look at the original input sequences.
@@ -719,6 +719,7 @@ run_pangolin
- description: Enable annotation of Pangolin lineages for a given build's subsampled sequences.
- default: ``false``
+.. _workflow-config-mask:
mask
----
@@ -772,6 +773,10 @@ min_length
- description: Minimum number of valid nucleotides (A, C, T, or G) for a genome to be included in the analysis by ``augur filter --min-length``.
- default: ``27000``
+.. note::
+ The ``min_length`` filter is applied to the **masked** sequences, not the original input sequences.
+ Depending on your :ref:`mask config parameters <workflow-config-mask>`, the masked sequences may contain more Ns than the original sequences and fail the ``min_length`` filter.
+
exclude_where
~~~~~~~~~~~~~
