Gcgi 1413 move failed report plugin to summary #489
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* Update default sample names and placeholder IDs/purity * Simplify by removing the benchmark_params.json file
Update 1.7.8 with latest changes from main
Add new JSON diff script and tests
Gcgi 1472 grab all patient ids
…manual-ids Allowed tumour and normal ids to be manually specified for provenance helper
…TS40X Added oncokb definitions to 40x assays
* Debugging * Debugging * Update clinically relevant variants count to reflect unique fusions after filtering by OncoKB levels * Update test checksum --------- Co-authored-by: Oumaima Hamza <[email protected]>
…ing undefined, which causes an error
self.patient_id_raw defaults to None when not in use
* Dump to json output * Process fusions and generate blob URLs from json template * gzip instead of pysam * skip header to use index * debugging * Fix column names * debugging * Fix genes combination scenario * Get template json * Specify path to file under plugin dir * no message * template json path * debugging * Reformat breakpoint * Search for bam and bai files * Use Node.js script for compression * Get tumour ID * Add positional argument * Add compression script relative path * Fix path * Change to CommonJS syntax * Add js scripts for compression * Convert to to CommonJS syntax * convert to CommonJS syntax * Compression using pysam.bgzip * base64 encoding * Convert into URL safe base64 * Mimic the JavaScript behavior * Fix blob URL format * Fix base64 encode * Compress json not the path to the file * Change whizbam URL * Change csv to tsv file * Fix and refactor fusion test * Changelog * Respond to PR comments: Improve warning/error messages and replace hardcoded values with variables * Clean up process_fusion function by adding helper functions * Add custom error class * Add whizbam_project parameter to the fusion plugin * Optimizing checks for files existence and URL assignment * Fix warning logging --------- Co-authored-by: Oumaima Hamza <[email protected]>
* Update changelog and version.py * Revert "Update changelog and version.py" This reverts commit 97bf3d7. * Update changelog and djerba version * Revert "Update changelog and djerba version" This reverts commit 26e27ac. * Update changelog and djerba version --------- Co-authored-by: Oumaima Hamza <[email protected]>
Fusion plugin test fixup
…s://github.com/oicr-gsi/djerba into GCGI-1413_move-failed-report-plugin-to-summary Merged with changes from local
iainrb
approved these changes
Jan 13, 2025
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Bitbucket incoming
Did not run mini djerba tests