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Substantial rewrite of the pipeline #32

Merged
merged 54 commits into from
Jun 7, 2024
Merged

Substantial rewrite of the pipeline #32

merged 54 commits into from
Jun 7, 2024

Commits on May 30, 2024

  1. Add subworkflow to validate samplesheets

    @robomics
    robomics committed May 30, 2024
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  2. Add subworkflow to process TADs

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    robomics committed May 30, 2024
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  3. Add subworkflow to run NCHG

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    robomics committed May 30, 2024
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  4. Refactor

    @robomics
    robomics committed May 30, 2024
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  5. Add subworkflow to run call TAD cliques

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    robomics committed May 30, 2024
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  6. Update main.nf and nextflow.config

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    robomics committed May 30, 2024
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  7. Add new Dockerfiles

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    robomics committed May 30, 2024
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  8. Update env.yml

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    robomics committed May 30, 2024
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  9. Remove unnecessary import

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    robomics committed May 30, 2024
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  10. Update base config

    @robomics
    robomics committed May 30, 2024
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  11. Remove debug code

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    robomics committed May 30, 2024
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  12. Update dependabot

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    robomics committed May 30, 2024
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  13. Update CI

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    robomics committed May 30, 2024
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  14. Merge branch 'main' into rewrite

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    robomics committed May 30, 2024
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  15. Merge branch 'main' into rewrite

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    robomics committed May 30, 2024
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  16. Update container uris in nextflow.config

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    robomics committed May 30, 2024
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  17. Bugfix

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    robomics committed May 30, 2024
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  18. Bugfix

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    robomics committed May 30, 2024
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  19. Merge branch 'main' into rewrite

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    robomics committed May 30, 2024
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  20. Add missing tag

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    robomics committed May 30, 2024
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  21. Merge branch 'main' into rewrite

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    robomics committed May 30, 2024
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Commits on May 31, 2024

  1. Debugging

    @robomics
    robomics committed May 31, 2024
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  2. Debugging

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    robomics committed May 31, 2024
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  3. Remove debug code

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    robomics committed May 31, 2024
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  4. Speed up CI

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    robomics committed May 31, 2024
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  5. Bugfix

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    robomics committed May 31, 2024
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  6. Fail CI on test dataset cache miss

    @robomics
    robomics committed May 31, 2024
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  7. Update NCHG Dockerfile

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    robomics committed May 31, 2024
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  8. Update test config

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    robomics committed May 31, 2024
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  9. Merge branch 'main' into rewrite

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    robomics committed May 31, 2024
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Commits on Jun 3, 2024

  1. Update apply_normalization.py

    @robomics
    robomics committed Jun 3, 2024
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  2. Update plot_maximal_clique_sizes.py

    @robomics
    robomics committed Jun 3, 2024
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  3. Update NCHG subworkflow

    @robomics
    robomics committed Jun 3, 2024
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  4. Update cliques workflow

    @robomics
    robomics committed Jun 3, 2024
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  5. Bugfix

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    robomics committed Jun 3, 2024
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  6. Bugfix

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    robomics committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. Bugfix

    @robomics
    robomics committed Jun 4, 2024
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  2. Merge branch 'main' into rewrite

    @robomics
    robomics committed Jun 4, 2024
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  3. Update nextflow.config

    @robomics
    robomics committed Jun 4, 2024
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  4. Add label process_very_high

    @robomics
    robomics committed Jun 4, 2024
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  5. Let call_cliques.py run for longer

    @robomics
    robomics committed Jun 4, 2024
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  6. Refactor

    @robomics
    robomics committed Jun 4, 2024
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  7. Support specifying different cutoffs for cis and trans cliques

    @robomics
    robomics committed Jun 4, 2024
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  8. Merge branch 'main' into rewrite

    @robomics
    robomics committed Jun 4, 2024
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  9. Update CI

    @robomics
    robomics committed Jun 4, 2024
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  10. Bugfix

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    robomics committed Jun 4, 2024
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  11. Bugfix

    @robomics
    robomics committed Jun 4, 2024
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Commits on Jun 5, 2024

  1. Bugfix

    @robomics
    robomics committed Jun 5, 2024
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  2. Update cliques workflow

    @robomics
    robomics committed Jun 5, 2024
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Commits on Jun 6, 2024

  1. Output NCHG expected values

    @robomics
    robomics committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. Bugfix

    @robomics
    robomics committed Jun 7, 2024
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  2. Update plot_significant_interactions.py

    @robomics
    robomics committed Jun 7, 2024
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  3. Update README

    @robomics
    robomics committed Jun 7, 2024
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  4. Update nextflow.config

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    robomics committed Jun 7, 2024
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