Feature/annotation tests #82
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…at change, added first test for annotation pipeline.
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commit 99ed88e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon May 13 13:14:16 2024 +0200 Feature/annotation tests (#82) * Create test skeleton for annotations * added annotation script to deeprvat setup, updated docs to reflect that change, added first test for annotation pipeline. * added tests for annotation pipeline, variant file now parquet * added data for test * added data for tests * Test for merge_deeprsea_pcas function * added test for absplice score aggregation * added robustness for mixed entry types in ID column of input vcf, created test case * added further tests * added pyranges to environment * Update absplice.yaml * Update environment_spliceai_rocksdb.yaml --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Mück <m991k@b260-pc003.inet.dkfz-heidelberg.de> Co-authored-by: PMBio <PMBio@users.noreply.github.com>
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commit 99ed88e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon May 13 13:14:16 2024 +0200 Feature/annotation tests (#82) * Create test skeleton for annotations * added annotation script to deeprvat setup, updated docs to reflect that change, added first test for annotation pipeline. * added tests for annotation pipeline, variant file now parquet * added data for test * added data for tests * Test for merge_deeprsea_pcas function * added test for absplice score aggregation * added robustness for mixed entry types in ID column of input vcf, created test case * added further tests * added pyranges to environment * Update absplice.yaml * Update environment_spliceai_rocksdb.yaml --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Mück <m991k@b260-pc003.inet.dkfz-heidelberg.de> Co-authored-by: PMBio <PMBio@users.noreply.github.com>
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commit 5715e99 Author: Marcel Mück <mueckm1@gmail.com> Date: Tue May 14 09:30:02 2024 +0200 Fix omitted variants, correct test cases. (#84) * addert assert to make sure no variants are omitted when merging annotations * changed expected files, sorts input files in aggregate_abscores * fixup! Format Python code with psf/black pull_request --------- Co-authored-by: “Marcel-Mueck” <“mueckm1@gmail.com”> Co-authored-by: PMBio <PMBio@users.noreply.github.com> commit 6f04801 Author: Kayla Meyer <129152803+meyerkm@users.noreply.github.com> Date: Mon May 13 14:49:59 2024 +0200 Revert "Feature streamline cv training" (#79) * Revert "Feature streamline cv training (#71)" This reverts commit d9ede28. * Add in association-only flag in rule config. Add in rule evaluate to complete cv-training-association-testing pipeline. * n_avg_chunks = 1 --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Eva Holtkamp <eva.holtkamp@gmx.de> commit 99ed88e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon May 13 13:14:16 2024 +0200 Feature/annotation tests (#82) * Create test skeleton for annotations * added annotation script to deeprvat setup, updated docs to reflect that change, added first test for annotation pipeline. * added tests for annotation pipeline, variant file now parquet * added data for test * added data for tests * Test for merge_deeprsea_pcas function * added test for absplice score aggregation * added robustness for mixed entry types in ID column of input vcf, created test case * added further tests * added pyranges to environment * Update absplice.yaml * Update environment_spliceai_rocksdb.yaml --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Mück <m991k@b260-pc003.inet.dkfz-heidelberg.de> Co-authored-by: PMBio <PMBio@users.noreply.github.com>
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commit 5715e99 Author: Marcel Mück <mueckm1@gmail.com> Date: Tue May 14 09:30:02 2024 +0200 Fix omitted variants, correct test cases. (#84) * addert assert to make sure no variants are omitted when merging annotations * changed expected files, sorts input files in aggregate_abscores * fixup! Format Python code with psf/black pull_request --------- Co-authored-by: “Marcel-Mueck” <“mueckm1@gmail.com”> Co-authored-by: PMBio <PMBio@users.noreply.github.com> commit 6f04801 Author: Kayla Meyer <129152803+meyerkm@users.noreply.github.com> Date: Mon May 13 14:49:59 2024 +0200 Revert "Feature streamline cv training" (#79) * Revert "Feature streamline cv training (#71)" This reverts commit d9ede28. * Add in association-only flag in rule config. Add in rule evaluate to complete cv-training-association-testing pipeline. * n_avg_chunks = 1 --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Eva Holtkamp <eva.holtkamp@gmx.de> commit 99ed88e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon May 13 13:14:16 2024 +0200 Feature/annotation tests (#82) * Create test skeleton for annotations * added annotation script to deeprvat setup, updated docs to reflect that change, added first test for annotation pipeline. * added tests for annotation pipeline, variant file now parquet * added data for test * added data for tests * Test for merge_deeprsea_pcas function * added test for absplice score aggregation * added robustness for mixed entry types in ID column of input vcf, created test case * added further tests * added pyranges to environment * Update absplice.yaml * Update environment_spliceai_rocksdb.yaml --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Mück <m991k@b260-pc003.inet.dkfz-heidelberg.de> Co-authored-by: PMBio <PMBio@users.noreply.github.com>
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* Use dynamic paths from rules for preprocessing pipeline * Rename * Use black dag * Update preprocessing.md Fix link * Snakefmt pipelines * Squashed commit of the following: commit 99ed88e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon May 13 13:14:16 2024 +0200 Feature/annotation tests (#82) * Create test skeleton for annotations * added annotation script to deeprvat setup, updated docs to reflect that change, added first test for annotation pipeline. * added tests for annotation pipeline, variant file now parquet * added data for test * added data for tests * Test for merge_deeprsea_pcas function * added test for absplice score aggregation * added robustness for mixed entry types in ID column of input vcf, created test case * added further tests * added pyranges to environment * Update absplice.yaml * Update environment_spliceai_rocksdb.yaml --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Mück <m991k@b260-pc003.inet.dkfz-heidelberg.de> Co-authored-by: PMBio <PMBio@users.noreply.github.com> * Revert "Squashed commit of the following:" This reverts commit 011273c. * Squashed commit of the following: commit 5715e99 Author: Marcel Mück <mueckm1@gmail.com> Date: Tue May 14 09:30:02 2024 +0200 Fix omitted variants, correct test cases. (#84) * addert assert to make sure no variants are omitted when merging annotations * changed expected files, sorts input files in aggregate_abscores * fixup! Format Python code with psf/black pull_request --------- Co-authored-by: “Marcel-Mueck” <“mueckm1@gmail.com”> Co-authored-by: PMBio <PMBio@users.noreply.github.com> commit 6f04801 Author: Kayla Meyer <129152803+meyerkm@users.noreply.github.com> Date: Mon May 13 14:49:59 2024 +0200 Revert "Feature streamline cv training" (#79) * Revert "Feature streamline cv training (#71)" This reverts commit d9ede28. * Add in association-only flag in rule config. Add in rule evaluate to complete cv-training-association-testing pipeline. * n_avg_chunks = 1 --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Eva Holtkamp <eva.holtkamp@gmx.de> commit 99ed88e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon May 13 13:14:16 2024 +0200 Feature/annotation tests (#82) * Create test skeleton for annotations * added annotation script to deeprvat setup, updated docs to reflect that change, added first test for annotation pipeline. * added tests for annotation pipeline, variant file now parquet * added data for test * added data for tests * Test for merge_deeprsea_pcas function * added test for absplice score aggregation * added robustness for mixed entry types in ID column of input vcf, created test case * added further tests * added pyranges to environment * Update absplice.yaml * Update environment_spliceai_rocksdb.yaml --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Mück <m991k@b260-pc003.inet.dkfz-heidelberg.de> Co-authored-by: PMBio <PMBio@users.noreply.github.com> * Revert "Squashed commit of the following:" This reverts commit 8ad84ea.
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* add pytest to env * Set workdir to repo So we can run the tests from anyhwere * Add string sample Update test data * Fix sample names * Add SAM prefix * add xdist run * don't cast samples to ints * fixup! Format Python code with psf/black pull_request * Add sample str test to process_sparse_gt test * Remove used import and variable * update pytest * update gh runner * Fix xdist version * Downgrade xdist * Squashed commit of the following: commit 99ed88e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon May 13 13:14:16 2024 +0200 Feature/annotation tests (#82) * Create test skeleton for annotations * added annotation script to deeprvat setup, updated docs to reflect that change, added first test for annotation pipeline. * added tests for annotation pipeline, variant file now parquet * added data for test * added data for tests * Test for merge_deeprsea_pcas function * added test for absplice score aggregation * added robustness for mixed entry types in ID column of input vcf, created test case * added further tests * added pyranges to environment * Update absplice.yaml * Update environment_spliceai_rocksdb.yaml --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Mück <m991k@b260-pc003.inet.dkfz-heidelberg.de> Co-authored-by: PMBio <PMBio@users.noreply.github.com> * Revert "Squashed commit of the following:" This reverts commit 5ce3e77. * Squashed commit of the following: commit 5715e99 Author: Marcel Mück <mueckm1@gmail.com> Date: Tue May 14 09:30:02 2024 +0200 Fix omitted variants, correct test cases. (#84) * addert assert to make sure no variants are omitted when merging annotations * changed expected files, sorts input files in aggregate_abscores * fixup! Format Python code with psf/black pull_request --------- Co-authored-by: “Marcel-Mueck” <“mueckm1@gmail.com”> Co-authored-by: PMBio <PMBio@users.noreply.github.com> commit 6f04801 Author: Kayla Meyer <129152803+meyerkm@users.noreply.github.com> Date: Mon May 13 14:49:59 2024 +0200 Revert "Feature streamline cv training" (#79) * Revert "Feature streamline cv training (#71)" This reverts commit d9ede28. * Add in association-only flag in rule config. Add in rule evaluate to complete cv-training-association-testing pipeline. * n_avg_chunks = 1 --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Eva Holtkamp <eva.holtkamp@gmx.de> commit 99ed88e Author: Marcel Mück <mueckm1@gmail.com> Date: Mon May 13 13:14:16 2024 +0200 Feature/annotation tests (#82) * Create test skeleton for annotations * added annotation script to deeprvat setup, updated docs to reflect that change, added first test for annotation pipeline. * added tests for annotation pipeline, variant file now parquet * added data for test * added data for tests * Test for merge_deeprsea_pcas function * added test for absplice score aggregation * added robustness for mixed entry types in ID column of input vcf, created test case * added further tests * added pyranges to environment * Update absplice.yaml * Update environment_spliceai_rocksdb.yaml --------- Co-authored-by: Magnus Wahlberg <endast@gmail.com> Co-authored-by: Mück <m991k@b260-pc003.inet.dkfz-heidelberg.de> Co-authored-by: PMBio <PMBio@users.noreply.github.com> * Revert "Squashed commit of the following:" This reverts commit 1d0bd6d. * Update micromamba * Use xdist for annotation tests * Move above comment * Lock ubuntu version * Cleanup yaml * Lock down ubuntu --------- Co-authored-by: PMBio <PMBio@users.noreply.github.com>
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