Scib artifact metrics - Githubissues

ASAP-CRN / pmdbs-sc-rnaseq-wf

Repo for testing and developing a common postmortem-derived brain sequencing (PMDBS) workflow harmonized across ASAP

Apache License 2.0

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Scib artifact metrics #45

Closed ergonyc closed 5 months ago

ergonyc commented 6 months ago

adds two additional scripts to execute:

add_harmony.py : make sure that we have PCA obsm available, and perform hamony integration.
artifact_metrics : calculate scib metrics on the final dataset and export report

WDL changes #46

[ ] to create the output assessment report add calls to
- [ ] "add_harmony.py" and
- [ ] "artifact_metrics.py"
[ ] add "--output-validation-file" arguments to
- [ ] "plot_qc_metrics.py",
- [ ] "filter.py" and
- [ ] "process.py"