Update cellranger tool

Allow the user to specify the chemistry parameter when running cellranger_count_metadata pipeline Update docs: add optional columns in cellranger_count_metadata section of the Pipelines page
vib-singlecell-nf · Sep 9, 2020 · 334137d · 334137d
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diff --git a/docs/pipelines.rst b/docs/pipelines.rst
@@ -250,7 +250,9 @@ and a metadata table:
 
 Optional columns:
 
-- ``short_uuid``: ``sample_name`` will be prefix by this value. This should be the same between sequencing runs of the same biological replicate 
+- ``short_uuid``: ``sample_name`` will be prefix by this value. This should be the same between sequencing runs of the same biological replicate
+- ``expect_cells``: This number will be used as argument for the ``--expect-cells`` parameter in ``cellranger count`.
+- ``chemistry``: This chemistry will be used as argument for the ``--chemistry`` parameter in ``cellranger count`.
 
 and a config:
 

diff --git a/src/cellranger b/src/cellranger
+34 −10		processes/count.nf
+10 −2		workflows/cellRangerCountWithMetadata.nf