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Rearrange processes and modules, add SV workflow for Delly2 #8

Merged
merged 42 commits into from
Aug 7, 2024
Merged

Rearrange processes and modules, add SV workflow for Delly2 #8

merged 42 commits into from
Aug 7, 2024

Commits on Jul 24, 2024

  1. Rename workflow to snv_annotations, absorb Funcotator

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  2. s/RepeatMasker-v3.0.1/RepeatMasker-3.0.1/

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  3. Use stablelift image from main

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  4. Add original copy of extract-vcf-features-SV.R

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  5. Add --output-rds argument

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  6. Add workflow for SV

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  7. Refactor, support SV and SNV

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  8. Add stubs to all processes

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  9. Bugfix, need leading params

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  10. Bugfix, remove module/ from relative path

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  11. Remove redundant process

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  12. Bugfix, clean up an undefined stub variable

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  13. Bugfix, clean up more undefined stub variables

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  14. Get rid of variables in utils module

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  15. Clean up variables in sv_workflow.nf

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  16. Clean up variables in snv_workflow.nf

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  17. Clean up variables in snv_annotations.nf

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  18. Replace colons with slashes

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  19. Combine intermediate files

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  20. Rename NFTest case as SNV-specific

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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  21. Add SV-specific NFTest, bugfix for parameters

    @nwiltsie
    nwiltsie committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. Bundle rtracklayer into Docker

    @nwiltsie
    nwiltsie committed Jul 25, 2024
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  2. Group arguments in Dockerfile

    @nwiltsie
    nwiltsie committed Jul 25, 2024
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  3. Small bugfixes

    @nwiltsie
    nwiltsie committed Jul 25, 2024
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  4. Pre-copy folder to standard path

    @nwiltsie
    nwiltsie committed Jul 25, 2024
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  5. Remove quotes

    @nwiltsie
    nwiltsie committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. Try a different mechanism to get library paths

    @nwiltsie
    nwiltsie committed Jul 26, 2024
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  2. Use branch version of image

    @nwiltsie
    nwiltsie committed Jul 26, 2024
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  3. Bugfixes, test cleanup for SV case

    @nwiltsie
    nwiltsie committed Jul 26, 2024
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Commits on Jul 29, 2024

  1. Add mermaid flow diagram

    @nwiltsie
    nwiltsie committed Jul 29, 2024
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  2. Add output at end of pipeline

    @nwiltsie
    nwiltsie committed Jul 29, 2024
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  3. Pull in latest changes to predict-liftover-stability.R

    @nwiltsie
    nwiltsie committed Jul 29, 2024
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  4. Bugfix, channel mis-match

    @nwiltsie
    nwiltsie committed Jul 29, 2024
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  5. Update CHANGELOG

    @nwiltsie
    nwiltsie committed Jul 29, 2024
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  6. Fix lints

    @nwiltsie
    nwiltsie committed Jul 29, 2024
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  7. Sort VCF after liftover in SV branch

    @nwiltsie
    nwiltsie committed Jul 29, 2024
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Commits on Aug 2, 2024

  1. Reword 'Variant Caller' to 'Variant Type'

    @nwiltsie
    nwiltsie committed Aug 2, 2024
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  2. Remove unused R function

    @nwiltsie
    nwiltsie committed Aug 2, 2024
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  3. s/run_sv_liftover/liftover_SV_StableLift/

    @nwiltsie
    nwiltsie committed Aug 2, 2024
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  4. s/run_intersect_gnomad/annotate_gnomAD_StableLift/

    @nwiltsie
    nwiltsie committed Aug 2, 2024
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Commits on Aug 6, 2024

  1. Add 'StableLift-${manifest.version}' to output_dir_base

    @nwiltsie
    nwiltsie committed Aug 6, 2024
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  2. Use wildcards for aptitude package build versions

    @nwiltsie
    nwiltsie committed Aug 6, 2024
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