ATAC QC component #868
Open
ATAC QC component #868
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
DriesSchaumont
requested changes
Oct 4, 2024
Comment on lines
+105
to
+111
| - type: python | ||
| __merge__: [/src/base/requirements/anndata_mudata.yaml, .] | ||
| packages: | ||
| - numpy~=1.23.5 | ||
| - scanpy~=1.9.3 | ||
| - muon~=0.1.5 | ||
| - pysam~=0.22.0 |
There was a problem hiding this comment.
We have a base version for scanpy. Also, the anndata_mudata base already pins numpy < 2
Suggested change
| - type: python | |
| __merge__: [/src/base/requirements/anndata_mudata.yaml, .] | |
| packages: | |
| - numpy~=1.23.5 | |
| - scanpy~=1.9.3 | |
| - muon~=0.1.5 | |
| - pysam~=0.22.0 | |
| - type: python | |
| __merge__: [/src/base/requirements/anndata_mudata.yaml, .] | |
| __merge__: [ /src/base/requirements/scanpy.yaml, .] | |
| packages: | |
| - muon~=0.1.5 | |
| - pysam~=0.22.0 |
| - pysam~=0.22.0 | ||
| test_setup: | ||
| - type: python | ||
| __merge__: [ /src/base/requirements/viashpy.yaml, /src/base/requirements/scanpy.yaml, .] |
There was a problem hiding this comment.
Because scanpy is already included in the regular setup, it should not be added again. (test setup steps are added on top of the regular setup)
Suggested change
| __merge__: [ /src/base/requirements/viashpy.yaml, /src/base/requirements/scanpy.yaml, .] | |
| __merge__: [ /src/base/requirements/viashpy.yaml, .] |
| mdata = mu.read(par["input"]) | ||
|
|
||
| logger.debug("Making var names unique") | ||
| mdata.var_names_make_unique() |
There was a problem hiding this comment.
I think I want to avoid calling this here
| atac.obs.drop(col, axis=1, inplace=True) | ||
|
|
||
| logger.info("Calculating QC metrics") | ||
| sc.pp.calculate_qc_metrics(atac, percent_top=None, log1p=False, inplace=True, layer=par["layer"]) |
There was a problem hiding this comment.
I want to avoid that things get overwritten by scanpy, could you pass a copy of the data?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changelog
Add component for calculating QC metrics for ATAC data.
Issue ticket number and link
Contributes to #398
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributor's guide
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI tests succeed!