Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

groHMM overhaul #165

Merged
merged 54 commits into from
Oct 23, 2024
Merged

groHMM overhaul #165

merged 54 commits into from
Oct 23, 2024

Commits on Oct 21, 2024

  1. style: Run styler

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    1df35bd View commit details
    Browse the repository at this point in the history

  2. test: Write grohmm tests

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    f7ddbb6 View commit details
    Browse the repository at this point in the history

  3. fix(grohmm): bam => bams

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    21ba6f7 View commit details
    Browse the repository at this point in the history

  4. fix(grohmm): Link up tuning files and samples

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    39265aa View commit details
    Browse the repository at this point in the history

  5. refactor(grohmm): Add notes of brainstorming

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    f431c73 View commit details
    Browse the repository at this point in the history

  6. feat: Add grohmm min and max tuning params

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    727fdd1 View commit details
    Browse the repository at this point in the history

  7. fix: of => fromList

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    bb59488 View commit details
    Browse the repository at this point in the history

  8. refactor(grohmm): Use parameter tuning split

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    ab20315 View commit details
    Browse the repository at this point in the history

  9. fix(grohmm): Use windowAnalysis 

    Apparently we weren't doing this. It's in the guidelines and in Shayne's scripts
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    6e0b9a8 View commit details
    Browse the repository at this point in the history

  10. refactor: Setup transcript calling

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    114136c View commit details
    Browse the repository at this point in the history

  11. build: Build a seperate grohmm conda package

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    d72402b View commit details
    Browse the repository at this point in the history

  12. chore: Add working

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    ce1c512 View commit details
    Browse the repository at this point in the history

  13. build(grohmm): Add Seqera containers

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    6ba858f View commit details
    Browse the repository at this point in the history

  14. test(grohmm): Add chr7 gtf

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    46646f0 View commit details
    Browse the repository at this point in the history

  15. test: Setup tests for grohmm

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    2ad3b9c View commit details
    Browse the repository at this point in the history

  16. chore(grohmm): Add example tuning evals from tutorial

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    65d16d0 View commit details
    Browse the repository at this point in the history

  17. fix(grohmm): Try removing any genes from "random" Chromosome

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    e221791 View commit details
    Browse the repository at this point in the history

  18. test(grohmm): Use kgChr7 gtf

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    0691cba View commit details
    Browse the repository at this point in the history

  19. test: Try it with refGene again

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    692e688 View commit details
    Browse the repository at this point in the history

  20. fix(grohmm): Set memory.limit

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    d965491 View commit details
    Browse the repository at this point in the history

  21. fix(grohmm): Remove keytype 

    It's in the vignette but the actual function call and docs don't have a
use for it. It just defaults to gene_id.
https://github.com/bioinformaticsorphanage/groHMM/blob/86486c388d12a636041c1fc40d1308f96abb5161/R/makeConsensusAnnotations.R#L47-L53
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    013978d View commit details
    Browse the repository at this point in the history

  22. refactor(grohmm): Get jobs running for every set of possibilities

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    af3cba8 View commit details
    Browse the repository at this point in the history

  23. test(grohmm): Test the whole subworkflow

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    a5e2bcc View commit details
    Browse the repository at this point in the history

  24. fix(grohmm): Give up on taking a tuning file 

    Can't support everything, if you're gonna run groHMM, you're just going
to run the tuning. If you want to minimize the runs, set the
grohmm_{min,max}_uts, and grohmm_{min,max}_ltprobb variables to the
desired values
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    7807899 View commit details
    Browse the repository at this point in the history

  25. test(grohmm): Fix how the channel is created to avoid exhausting it 

    https://midnighter.github.io/nextflow-gotchas/gotchas/singleton-channel/
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    d67acde View commit details
    Browse the repository at this point in the history

  26. fix(grohmm): Get transcript calling running

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    09212f9 View commit details
    Browse the repository at this point in the history

  27. fix(grohmm): Clean up tuning file to match

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    d2e4065 View commit details
    Browse the repository at this point in the history

  28. fix(grohmm): Update groHMM with fix 

    Now it handles when there are no broken transcripts(ie with a test dataset)
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    2286b7a View commit details
    Browse the repository at this point in the history

  29. Add consensus bed as output for testing

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    9388a21 View commit details
    Browse the repository at this point in the history

  30. test(grohmm): Update all the snapshots

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    b7567c8 View commit details
    Browse the repository at this point in the history

  31. refactor(grohmm): Use each input 

    Didn't know that was a thing!
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    baa008b View commit details
    Browse the repository at this point in the history

  32. feat(grohmm): Add Native MultiQC support

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    d9e94aa View commit details
    Browse the repository at this point in the history

  33. fix(grohmm): Update labels for parametertuning 

    Since these are are split into seperate jobs now, they're not
"long"(longest I've seen one take is ~143 minutes).

Adding arrays later because there's so many of them and they're the same
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    a535c8c View commit details
    Browse the repository at this point in the history

  34. chore: Add a note about the subworkflow functionality

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    2f1c81c View commit details
    Browse the repository at this point in the history

  35. chore: oras => https

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    cd9151e View commit details
    Browse the repository at this point in the history

  36. refactor(grohmm): Use each input 

    Didn't know that was a thing!
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    26626fa View commit details
    Browse the repository at this point in the history

  37. test(grohmm): Write a failing test 

    With the help of cursor
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    9272060 View commit details
    Browse the repository at this point in the history

  38. fix(grohmm): Update to work with CHM13 

    refactor: Clean up code more
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    3d5cf85 View commit details
    Browse the repository at this point in the history

  39. refactor: Replace jpg with png

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    b8548a3 View commit details
    Browse the repository at this point in the history

  40. test: Remove skip_tuning test

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    0c7a9ba View commit details
    Browse the repository at this point in the history

  41. test: Bump snapshot

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    0958778 View commit details
    Browse the repository at this point in the history

  42. Update CHANGELOG

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    d17d9df View commit details
    Browse the repository at this point in the history

  43. docs: Update groHMM docs

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    3c947b0 View commit details
    Browse the repository at this point in the history

  44. fix(grohmm): Try calling no more than 10 cores

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    2b2b90f View commit details
    Browse the repository at this point in the history

  45. chore: Add a custom makeConsensusAnnotations function

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    e101553 View commit details
    Browse the repository at this point in the history

  46. Try creating a custom makeConsensusAnnotations and setup test

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    3028ae1 View commit details
    Browse the repository at this point in the history

  47. Get custom running

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    d4ac91f View commit details
    Browse the repository at this point in the history

  48. Start over

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    3444c5b View commit details
    Browse the repository at this point in the history

  49. refactor: Split into chunks

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    508452b View commit details
    Browse the repository at this point in the history

  50. More tests

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    b538a16 View commit details
    Browse the repository at this point in the history

  51. fix(grohmm): Support gxf 

    Scrap all of the CHM13 attempts

I think it's the gtf conversion stuff that's causing the memory
overload. But I can get them all to load locally. So I'm going to try to
use gff3 files, if they're supplied, otherwise fall back to gtf.
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    ef677b1 View commit details
    Browse the repository at this point in the history

  52. fix(chm13): Prevent some errors during transcriptcalling

    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    afbb7b6 View commit details
    Browse the repository at this point in the history

  53. style(grohmm): Clean up 

    Editorconfig, styler, consistant naming
    @edmundmiller
    edmundmiller committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    5c6b24a View commit details
    Browse the repository at this point in the history

Commits on Oct 22, 2024

  1. chore: Move test data to test-datasets repo

    @edmundmiller
    edmundmiller committed Oct 22, 2024
    Configuration menu
    Copy the full SHA
    9c65113 View commit details
    Browse the repository at this point in the history