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Organize into subworkflows #59

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Organize into subworkflows #59

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Commits on Dec 19, 2023

  1. Build: HOST_STAR Subworkflow 

    Co-authored-by: Mariana Dias Guilardi <[email protected]>
    @alyssa-ab @mariguilardi
    alyssa-ab and mariguilardi committed Dec 19, 2023
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  2. Build: HOST_STAR Subworkflow 

    Co-authored-by: Mariana Dias Guilardi <[email protected]>
    @alyssa-ab @mariguilardi
    alyssa-ab and mariguilardi committed Dec 19, 2023
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  3. host: add trimmers

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  4. Build: PLUS subworkflow 

    Co-authored-by: Mariana Guilardi <[email protected]>
    @alyssa-ab @mariguilardi
    alyssa-ab and mariguilardi committed Dec 19, 2023
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  5. HOST: remove unneeded emissions

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  6. PLUS: add junction emission

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  7. PLUS: Add samtools

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    alyssa-ab committed Dec 19, 2023
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  8. plus: add join bam_bai_junction 

    Co-authored-by: Mariana Dias Guilardi <[email protected]>
    @alyssa-ab @mariguilardi
    alyssa-ab and mariguilardi committed Dec 19, 2023
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  9. reorganize workflow with subworkflows 

    Co-authored-by: Mariana Guilardi <[email protected]>
    @alyssa-ab @mariguilardi
    alyssa-ab and mariguilardi committed Dec 19, 2023
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  10. subworkflows: rename STAR to match args 

    Co-authored-by: Mariana Guilardi <[email protected]>
    @alyssa-ab @mariguilardi
    alyssa-ab and mariguilardi committed Dec 19, 2023
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  11. clean up main workflow

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  12. build INSERTION_SITES subworkflow

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    alyssa-ab committed Dec 19, 2023
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  13. build: validate subworkflow

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    alyssa-ab committed Dec 19, 2023
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  14. fix(validate): Add log_final to make Multiqc happy

    @edmundmiller @alyssa-ab
    edmundmiller authored and alyssa-ab committed Dec 19, 2023
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  15. fix(host): add mqc_log for TRIMMOMATIC in MultiQC

    @alyssa-ab
    Alyssa Ann Briggs authored and alyssa-ab committed Dec 19, 2023
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  16. build chimeric reads subworkflow

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    Alyssa Ann Briggs authored and alyssa-ab committed Dec 19, 2023
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  17. Template update for nf-core/tools version 2.8

    @nf-core-bot @alyssa-ab
    nf-core-bot authored and alyssa-ab committed Dec 19, 2023
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  18. Template update for nf-core/tools version 2.9

    @nf-core-bot @alyssa-ab
    nf-core-bot authored and alyssa-ab committed Dec 19, 2023
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  19. bug fix: rollback star and samtools version

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  20. star/samtools: use matching mulled containers

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  21. fix: Remove samtools diffs 

    No reason to diverge from upstream on these, it's just a STAR problem.
    @edmundmiller @alyssa-ab
    edmundmiller authored and alyssa-ab committed Dec 19, 2023
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  22. fix prettier

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  23. fix prettier

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    alyssa-ab committed Dec 19, 2023
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  24. fix prettier + html functionality

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    alyssa-ab committed Dec 19, 2023
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  25. chore: bump date

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    alyssa-ab committed Dec 19, 2023
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  26. update README and modules.json

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  27. run prettier

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    alyssa-ab committed Dec 19, 2023
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  28. add nf-validaiton for input

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    alyssa-ab committed Dec 19, 2023
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  29. clean up README + CHANGELOG

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    alyssa-ab committed Dec 19, 2023
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  30. update gitignore

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    alyssa-ab committed Dec 19, 2023
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  31. fix linting

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    alyssa-ab committed Dec 19, 2023
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  32. fix linting

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  33. fix nf-test config/names/snapshot

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    alyssa-ab committed Dec 19, 2023
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  34. fix linting

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  35. Template update for nf-core/tools version 2.8

    @nf-core-bot @alyssa-ab
    nf-core-bot authored and alyssa-ab committed Dec 19, 2023
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  36. Template update for nf-core/tools version 2.9

    @nf-core-bot @alyssa-ab
    nf-core-bot authored and alyssa-ab committed Dec 19, 2023
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  37. bug fix: rollback star and samtools version

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  38. star/samtools: use matching mulled containers

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  39. update README and modules.json

    @alyssa-ab
    alyssa-ab committed Dec 19, 2023
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  40. update modules

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    alyssa-ab committed Dec 19, 2023
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  41. update snapshots of passing tests + script paths

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    alyssa-ab committed Dec 19, 2023
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  42. fix prettier

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    alyssa-ab committed Dec 19, 2023
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