Feature/atac demux #726
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Feature/atac demux #726
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Co-authored-by: Dries Schaumont <[email protected]>
Co-authored-by: Dries Schaumont <[email protected]>
DriesSchaumont
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…813) * preproc script * preproc script * tokenize and pad script * tokenize and pad script * embedding script * test resourcers and evaluation script * cross check gene set * pad_tokenize module * updat image * remove test resources, update inputs * use pytorch image * remove integration component * remove nvidia reqs * remove load_model option * Fix retag for viash-hub not using correct namespace separator (#745) * CI - Build: Fix second occurance of namespace separator (#746) * script to download scgpt test data * remove test resources script * adjust preprocessing script * add scgpt full preproc module * integration submodule * integration submodule and add normalize_total flag * add params * Add script to download scgpt test resources (#750) * add script to download scgpt test resources * Update resources_test_scripts/scgpt.sh Co-authored-by: Dries Schaumont <[email protected]> * add drive folders containing data and model * chmod +x --------- Co-authored-by: Dries Schaumont <[email protected]> * embedding module * add unit tests * undo subsampling test data * update tests * update tests * update memory requirements * update tests * update changelog * update component name * fix tests, update changelog * run tests on subsampled data * adjust shm size * update test * update memory requirements nextflow * update test * update test * update test * expand unit tests, update script with loggers and todo * Add ATAC demux (#726) * run tests with subsampled data * use specific model input files instead of directory * update test data * Remove muon as test dependency for concatenate_h5mu. (#773) * scGPT binning component (#765) Co-authored-by: Dries Schaumont <[email protected]> * update embedding dependencies and gene name layer handling * update input handling * include dsbn logic * update unit tests * update config * expand unit tests, fix dsbn * Update CHANGELOG.md Co-authored-by: Dries Schaumont <[email protected]> * Update src/scgpt/embedding/config.vsh.yaml Co-authored-by: Dries Schaumont <[email protected]> * update required, remove shared memory docker * Add scGPT padding and tokenization component (#754) * add module for scgpt padding and tokenization * remove base requirement * update changelog * update component name * expand unit tests, update script with loggers and todo * fix unit tests * remove annotation script * run tests with subsampled data * use specific model input files instead of directory * remove unused binning script * update layer names and handling * Add script to download scgpt test resources (#750) * add script to download scgpt test resources * Update resources_test_scripts/scgpt.sh Co-authored-by: Dries Schaumont <[email protected]> * add drive folders containing data and model * chmod +x --------- Co-authored-by: Dries Schaumont <[email protected]> * preproc script * preproc script * tokenize and pad script * tokenize and pad script * embedding script * test resourcers and evaluation script * cross check gene set * Fix retag for viash-hub not using correct namespace separator (#745) * CI - Build: Fix second occurance of namespace separator (#746) * script to download scgpt test data * remove test resources script * pad_tokenize module * updat image * remove test resources, update inputs * use pytorch image * remove integration component * remove nvidia reqs * remove load_model option * adjust preprocessing script * add scgpt full preproc module * integration submodule * integration submodule and add normalize_total flag * add params * update scanpy version * remove branch irrelevant scripts * update output handling * update unit tests, add output compression * update key name input output * fix test * update unit tests * Update CHANGELOG.md Co-authored-by: Dries Schaumont <[email protected]> * add pars to logging --------- Co-authored-by: Dries Schaumont <[email protected]> * enable gpu device option * update dsbn * remove temporary, unused components * update error messages, remove device param * remove dropout param * fix typo * fix typo * Generate scgpt cross check genes module (#758) * base script and config added * config extended + logger set up + tests in progress * config working + script improved + tests in progress * exception handling, extended tests * extended tests + better logging * changelog entry added * test resource path in config fixed * python test setup added to config * PR comments fixed * updated to use subset data * remove batch id column logic * update authors * resources, tests and dependencies fixes * update key name input output * update key name input output * update var gene names * update config * compression param added + minor fixes --------- Co-authored-by: dorien-er <[email protected]> Co-authored-by: DriesSchaumont <[email protected]> * undo concat changes --------- Co-authored-by: jakubmajercik <[email protected]> Co-authored-by: Dries Schaumont <[email protected]> Co-authored-by: Vladimir Shitov <[email protected]> Co-authored-by: Jakub Majercik <[email protected]>
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Changelog
reference/build_cellranger_arc_referencecomponent. It creates reference compatible with both Multiome (ATAC + RNA) and ATAC-only pipelines. For more information, check out cellranger documentationdemux/cellranger_atac_mkfastqcomponent for generation of fastq-files from bcl-filessrc/demux/cellranger_mkfastq/test.pyIssue 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!