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Save marker gene expression for cell-type-consensus module #130

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merged 8 commits into from
Feb 24, 2025

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allyhawkins
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@allyhawkins allyhawkins commented Feb 21, 2025

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 from OpenScPCA-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.

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Note that the test run succeeded and I checked the outputs looked correct in the bucket. This should be ready for review.

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LGTM!

@allyhawkins allyhawkins merged commit f6dcd0d into main Feb 24, 2025
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@allyhawkins allyhawkins deleted the allyhawkins/save-gene-expression branch February 24, 2025 18:37
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