Save marker gene expression for cell-type-consensus module #130
+128
−25
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Closes #128
Closes #125
This PR modifies the
cell-type-consensus
module to also export a table of logcounts for all marker genes used for validating cell types (see https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/main/analyses/cell-type-consensus/references/validation-markers.tsv). I copied over the script fromOpenScPCA-analysis
to incorporate the new changes for saving gene expression.For the workflow itself, I modified it to have two output files, one for consensus and one for marker genes. And then I added a new parameter for the marker gene file.
While I was here I updated the link for the consensus reference to use a tagged version again. I also had to update the consensus docker image since we are now using
scuttle
. I updated all the tags to v0.2.2 while I was at it.Once all the images for
OpenScPCA-analysis
v0.2.2 are finished building then I'll do a test run of the workflow.