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Save input files and logs #168

Merged
merged 34 commits into from
Mar 5, 2024
Merged

Save input files and logs #168

merged 34 commits into from
Mar 5, 2024

Commits on Feb 22, 2024

  1. Put CSVs generated for metapipeline in one directory

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  2. Add publishDir rules for saving generated config and for statu check … 

    …process logs
    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  3. Always save CSV for align-DNA

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  4. Always save YAML for call-gSNP

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  5. Always save CSV for call-gSV

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  6. Always save CSV for call-mtSNV

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  7. Always save YAML for call-sSNV

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  8. Always save YAML for call sSV

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  9. Save CSV for convert-BAM2FASTQ

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  10. Always save YAML for recalibrate-BAM

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  11. Always save YAML for targeted-coverage

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  12. Save logs for convert-BAM2FASTQ CSV creation

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  13. Save logs for call-mtSNV CSV creation

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  14. Update channel for passing CSV to call-mtSNV

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  15. Fix log saving in call-gSV

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  16. Update channel for passing CSV to call-gSV

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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  17. Update CSV channels to use named channels

    @yashpatel6
    yashpatel6 committed Feb 22, 2024
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Commits on Feb 23, 2024

  1. Save align-DNA process logs

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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  2. Save call-gSNP process logs

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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  3. Save call-gSV logs

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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  4. Save call-mtSNV process logs

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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  5. Add logs to output for mtsnv

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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  6. Save process logs for call-sSNV

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    yashpatel6 committed Feb 23, 2024
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  7. Save process logs for convert-BAM2FASTQ

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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  8. Save logs for call-sSV process

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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  9. Save process logs for recalibrate-BAM

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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  10. Save logs for targeted-coverage process

    @yashpatel6
    yashpatel6 committed Feb 23, 2024
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Commits on Feb 26, 2024

  1. Fix format for tuple emission

    @yashpatel6
    yashpatel6 committed Feb 26, 2024
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  2. Merge main into branch

    @yashpatel6
    yashpatel6 committed Feb 26, 2024
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  3. Save process logs for calculate targeted coverage run

    @yashpatel6
    yashpatel6 committed Feb 26, 2024
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Commits on Mar 1, 2024

  1. Merge branch 'main' of github.com:uclahs-cds/metapipeline-DNA into ya… 

    …shpatel-save-files-and-logs
    @yashpatel6
    yashpatel6 committed Mar 1, 2024
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Commits on Mar 4, 2024

  1. Add logdir for all pipeline processes

    @yashpatel6
    yashpatel6 committed Mar 4, 2024
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  2. Add log param to tests and update tests for call-sCNA

    @yashpatel6
    yashpatel6 committed Mar 4, 2024
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  3. Update CHANGELOG

    @yashpatel6
    yashpatel6 committed Mar 4, 2024
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