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Replace input CSV with YAML and parse sample ID from BAM #106

Merged
merged 20 commits into from
Aug 1, 2023
Merged

Replace input CSV with YAML and parse sample ID from BAM #106

merged 20 commits into from
Aug 1, 2023

Commits on Jul 24, 2023

  1. update submodules

    Mootor authored and Mootor committed Jul 24, 2023
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  2. remove CSV and add YAML input

    Mootor authored and Mootor committed Jul 24, 2023
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Commits on Jul 25, 2023

  1. add custom schema

    Mootor authored and Mootor committed Jul 25, 2023
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  2. udate ouput dir structure set up

    Mootor authored and Mootor committed Jul 25, 2023
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  3. change patient_id to sample_id

    Mootor authored and Mootor committed Jul 25, 2023
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  4. update pipeval

    Mootor authored and Mootor committed Jul 25, 2023
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  5. remove empty line

    Mootor authored and Mootor committed Jul 25, 2023
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  6. update channels to parse input from YAML

    Mootor authored and Mootor committed Jul 25, 2023
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  7. Update CHANGELOG.md

    Mootor authored and Mootor committed Jul 25, 2023
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  8. fix YAML linting

    Mootor authored and Mootor committed Jul 25, 2023
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  9. fix YAML linting

    Mootor authored and Mootor committed Jul 25, 2023
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  10. update help comments

    Mootor authored and Mootor committed Jul 25, 2023
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  11. remove redundant code

    Mootor authored and Mootor committed Jul 25, 2023
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  12. update comment in config

    Mootor authored and Mootor committed Jul 25, 2023
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  13. update logging

    Mootor authored and Mootor committed Jul 25, 2023
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  14. use params.samples_to_process to parse sample id

    Mootor authored and Mootor committed Jul 25, 2023
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Commits on Jul 26, 2023

  1. set sample ID from tumor ID extracted using params.samples_to_process

    Mootor authored and Mootor committed Jul 26, 2023
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  2. remove redundant code

    Mootor authored and Mootor committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. check for multiple tumor samples before setting sample param

    Mootor authored and Mootor committed Jul 27, 2023
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Commits on Aug 1, 2023

  1. fix typo in error

    Mootor authored and Mootor committed Aug 1, 2023
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