Ingestion integration tests #801
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… feature/no-ref/ingestion-integration-tests
… feature/no-ref/ingestion-integration-tests
…ion-integration-tests
DriesSchaumont
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Aug 2, 2024
DriesSchaumont
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Aug 6, 2024
dorien-er
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Aug 7, 2024
rcannood
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Aug 9, 2024
* wip porting updated bd_rhapsody * wip porting updated bd_rhapsody * wip converting updated bd rhapsody * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * fix config parsing * update convert script * fix unit tests * add build reference component * update resources test script * update resources test script * fix unit test build reference * fix unit test build reference * update test resources scripts * update test resources scripts * remove sleep * update unit tests * update unit tests with full test data * update unit tests with full test data * update test resources * Update test resource script * Update reference filename in config and scripts * Add celltypist and onclass test data added (#847) * Add scgpt test resources script (#800) Co-authored-by: Dorien <41797896+dorien-er@users.noreply.github.com> * Add reclaim-the-bytes to unit test CI * QC integration tests (#808) * from_h5mu_to_seurat: bump Seurat to latest version. (#850) * scgpt cell type annotation component (#798) * Extend integration tests for integration workflows (#801) * Remove deprecated filter_with_hvg component (#843) * fix shutil reference output * Reduce genome size * convert component * fix unit test bd_rhapsody2 * add bd_rhap2 workflow * fix workflow output * add integration tests * update convert for smk data * enable all params in bd_rhap2 workflow" * update resources test script for smk data * update resources test script for smk data * update resources test script for smk data * update resources test script for smk data * undo changes in original bd rhap reference script * resolve merge * undo smk tests * remove bd rhapsody v1.x workflow, replace with bd rhapsody v2.x * rename components * fixes to components * fix test * subset smk as well, fix calls * fix test * fix data processing and test * fix test * fix test --------- Co-authored-by: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com> Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com> Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
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Changelog
Outputs of ingestion workflows integration tests checked through standalone components.
Issue ticket number and link
Closes #xxxx (Replace xxxx with the GitHub issue number)
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I have performed a self-review of my code
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Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
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