Create SampleQC and Batching notebooks #744
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mwalker174
reviewed
Nov 14, 2024
Co-authored-by: Mark Walker <[email protected]>
Co-authored-by: Mark Walker <[email protected]>
Co-authored-by: Mark Walker <[email protected]>
mwalker174
requested changes
Nov 26, 2024
| "source": [ | ||
| "# Display metadata table, which was generated as part of EvidenceQC\n", | ||
| "PASS_METADATA = os.path.join(WS_BUCKET, \"evidence_qc/filtering/passed_samples_qc_metadata.tsv\")\n", | ||
| "pass_df = pd.read_table(PASS_METADATA)\n", |
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This is breaking on me:
FileNotFoundError: b/fc-41a63557-9ddf-41ba-b5d0-807be90ddb87/o/evidence_qc%2Ffiltering%2Fpassed_samples_qc_metadata.tsv
Does pandas support reading directly from buckets?
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Yes, it does - you need to use gs:// as a prefix though.
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Sorry, on closer inspection I realized that this is automatically set based on WS_BUCKET, which is pulled from os.environ['WORKSPACE_BUCKET']. Strange to me that this does not automatically prepend gs:// in this case though, as it does for me...do you mind sharing the value of WS_BUCKET in your notebook?
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Updated accordingly - file path now matches what is generated in the QC notebook.
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This PR introduces the initial set of
SampleQCandBatchingnotebooks part of the featured workspace into the GATK-SV repository to enable fine-grained source control. They have been added to the newly-createdscripts/notebooks/directory.