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Fix omitted variants, correct test cases. #84

Merged
merged 3 commits into from
May 14, 2024
Merged

Fix omitted variants, correct test cases. #84

merged 3 commits into from
May 14, 2024

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Marcel-Mueck
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@Marcel-Mueck Marcel-Mueck commented May 13, 2024 •
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What

This PR does three things:

Testing

performed automatically via github actions

@Marcel-Mueck Marcel-Mueck requested a review from endast May 13, 2024 20:18
endast
endast approved these changes May 14, 2024
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Looks good!

@Marcel-Mueck Marcel-Mueck merged commit 5715e99 into main May 14, 2024
1 check passed
@Marcel-Mueck Marcel-Mueck deleted the fix-omitted-variants branch May 14, 2024 07:30
endast added a commit that referenced this pull request May 14, 2024
@endast
Squashed commit of the following:
1d0bd6d 
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>
endast added a commit that referenced this pull request May 14, 2024
@endast
Squashed commit of the following:
8ad84ea 
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>
endast added a commit that referenced this pull request May 14, 2024
@endast
Use dynamic paths from rules for preprocessing pipeline (#83)
12edb1e 
* 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.
endast added a commit that referenced this pull request May 14, 2024
@endast
Add test data from str samples and speed up tests (#73)
77f268d 
* 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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@Marcel-Mueck @endast