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Sfitz by readgroup and add FastQC #62

Merged
merged 46 commits into from
Jul 19, 2024
Merged

Sfitz by readgroup and add FastQC #62

merged 46 commits into from
Jul 19, 2024

Commits on Jun 16, 2024

  1. process by readgroup in progress

    @sorelfitzgibbon
    sorelfitzgibbon committed Jun 16, 2024
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  2. standardize algorithms to algorithm

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    sorelfitzgibbon committed Jun 16, 2024
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  3. samtools stats by readgroup

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    sorelfitzgibbon committed Jun 16, 2024
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  4. update changelog

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    sorelfitzgibbon committed Jun 16, 2024
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  5. fix mislabel

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    sorelfitzgibbon committed Jun 16, 2024
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  6. revert unintentional resource changes

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    sorelfitzgibbon committed Jun 16, 2024
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  7. add fastqc

    @sorelfitzgibbon
    sorelfitzgibbon committed Jun 16, 2024
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  8. add fastqc module

    @sorelfitzgibbon
    sorelfitzgibbon committed Jun 16, 2024
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  9. use process_afterscript

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    sorelfitzgibbon committed Jun 16, 2024
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  10. update changelog

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    sorelfitzgibbon committed Jun 16, 2024
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  11. update nftest for fastqc

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    sorelfitzgibbon committed Jun 16, 2024
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  12. fix nftest path

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    sorelfitzgibbon committed Jun 16, 2024
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  13. merge with sfitz-by-readgroup complete and tested

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    sorelfitzgibbon committed Jun 16, 2024
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  14. use fastqc docker with samtools

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    sorelfitzgibbon committed Jun 16, 2024
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  15. fastqc by readgroup

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    sorelfitzgibbon committed Jun 16, 2024
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  16. nftest paths updated

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    sorelfitzgibbon committed Jun 16, 2024
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  17. refactor channels

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    sorelfitzgibbon committed Jun 16, 2024
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  18. add hg003 to NFTest

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    sorelfitzgibbon committed Jun 16, 2024
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  19. update samtools

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    sorelfitzgibbon committed Jun 16, 2024
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  20. pull main - samtools update

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    sorelfitzgibbon committed Jun 16, 2024
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  21. use fastqc docker with samtools

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    sorelfitzgibbon committed Jun 16, 2024
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  22. add fastqc resource allocations

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    sorelfitzgibbon committed Jun 16, 2024
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  23. add fastqc threading and adjust resources

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    sorelfitzgibbon committed Jun 16, 2024
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  24. add fastqc

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    sorelfitzgibbon committed Jun 16, 2024
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Commits on Jun 17, 2024

  1. add fastqc to metadata.yaml

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    sorelfitzgibbon committed Jun 17, 2024
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Commits on Jun 20, 2024

  1. Bump the pipeline-submodules group with 2 updates 

    Bumps the pipeline-submodules group with 2 updates: [external/pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module) and [external/pipeline-Nextflow-config](https://github.com/uclahs-cds/pipeline-Nextflow-config).


Updates `external/pipeline-Nextflow-module` from `ef40c10` to `537da32`
- [Commits](uclahs-cds/pipeline-Nextflow-module@ef40c10...537da32)

Updates `external/pipeline-Nextflow-config` from `be1eaf5` to `2127286`
- [Release notes](https://github.com/uclahs-cds/pipeline-Nextflow-config/releases)
- [Commits](uclahs-cds/pipeline-Nextflow-config@be1eaf5...2127286)

---
updated-dependencies:
- dependency-name: external/pipeline-Nextflow-module
  dependency-type: direct:production
  dependency-group: pipeline-submodules
- dependency-name: external/pipeline-Nextflow-config
  dependency-type: direct:production
  dependency-group: pipeline-submodules
...

Signed-off-by: dependabot[bot] <[email protected]>
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    dependabot[bot] authored and sorelfitzgibbon committed Jun 20, 2024
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  2. Merge branch 'main' into sfitz-by-readgroup

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    sorelfitzgibbon committed Jun 20, 2024
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  3. add final newline

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    sorelfitzgibbon committed Jun 20, 2024
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Commits on Jun 24, 2024

  1. update readme

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    sorelfitzgibbon committed Jun 24, 2024
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  2. update nftest.yml

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    sorelfitzgibbon committed Jun 24, 2024
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Commits on Jun 25, 2024

  1. parameterize fastqc and add max gps to stats

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    sorelfitzgibbon committed Jun 25, 2024
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  2. sanitize library ID

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    sorelfitzgibbon committed Jun 25, 2024
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  3. update test configs

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    sorelfitzgibbon committed Jun 25, 2024
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  4. change process input variable names

    @sorelfitzgibbon
    sorelfitzgibbon committed Jun 25, 2024
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  5. add slurm logs and extra test files to .gitignore

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    sorelfitzgibbon committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. update readme

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    sorelfitzgibbon committed Jun 26, 2024
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  2. update comments

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    sorelfitzgibbon committed Jun 26, 2024
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  3. adjust run level triggers

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    sorelfitzgibbon committed Jun 26, 2024
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  4. adjust log filename

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    sorelfitzgibbon committed Jun 26, 2024
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  5. update nftests

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    sorelfitzgibbon committed Jun 26, 2024
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  6. fix test name

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    sorelfitzgibbon committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. remove out of date comments

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    sorelfitzgibbon committed Jun 27, 2024
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  2. change process names

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    sorelfitzgibbon committed Jun 27, 2024
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  3. rename bamqc_outformat to bamqc_output_format

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    sorelfitzgibbon committed Jun 27, 2024
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  4. rename bamqc_outformat to bamqc_output_format

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    sorelfitzgibbon committed Jun 27, 2024
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  5. remove fastqc as default

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    sorelfitzgibbon committed Jun 27, 2024
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