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Grohmm overhaul #165

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Grohmm overhaul #165

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Commits on Oct 16, 2024

  1. style: Run styler

    @edmundmiller
    edmundmiller committed Oct 16, 2024
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  2. test: Write grohmm tests

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  3. fix(grohmm): bam => bams

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

    @edmundmiller
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  5. refactor(grohmm): Add notes of brainstorming

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  6. feat: Add grohmm min and max tuning params

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  7. fix: of => fromList

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  8. refactor(grohmm): Use parameter tuning split

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  9. fix(grohmm): Use windowAnalysis 

    Apparently we weren't doing this. It's in the guidelines and in Shayne's scripts
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  10. refactor: Setup transcript calling

    @edmundmiller
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  11. build: Build a seperate grohmm conda package

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  12. chore: Add working

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  13. build(grohmm): Add Seqera containers

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  14. test(grohmm): Add chr7 gtf

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  15. test: Setup tests for grohmm

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

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

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  18. test(grohmm): Use kgChr7 gtf

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  19. test: Try it with refGene again

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  20. fix(grohmm): Set memory.limit

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

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  23. test(grohmm): Test the whole subworkflow

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

    https://midnighter.github.io/nextflow-gotchas/gotchas/singleton-channel/
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  26. fix(grohmm): Get transcript calling running

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

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  28. fix(grohmm): Update groHMM with fix 

    Now it handles when there are no broken transcripts(ie with a test dataset)
    @edmundmiller
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Commits on Oct 18, 2024

  1. Add consensus bed as output for testing

    @edmundmiller
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  2. test(grohmm): Update all the snapshots

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  3. refactor(grohmm): Use each input 

    Didn't know that was a thing!
    @edmundmiller
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  4. feat(grohmm): Add Native MultiQC support

    @edmundmiller
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  5. 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
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  6. chore: Add a note about the subworkflow functionality

    @edmundmiller
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  7. chore: oras => https

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  8. refactor(grohmm): Use each input 

    Didn't know that was a thing!
    @edmundmiller
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  9. test(grohmm): Write a failing test 

    With the help of cursor
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  10. fix(grohmm): Update to work with CHM13 

    refactor: Clean up code more
    @edmundmiller
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  11. refactor: Replace jpg with png

    @edmundmiller
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  12. test: Remove skip_tuning test

    @edmundmiller
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  13. test: Bump snapshot

    @edmundmiller
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  14. fix(multiqc): Update groHMM plot fn

    @edmundmiller
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  15. Update CHANGELOG

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    edmundmiller committed Oct 18, 2024
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  16. docs: Update groHMM docs

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

    @edmundmiller
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  18. chore: Add a custom makeConsensusAnnotations function

    @edmundmiller
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  19. Try creating a custom makeConsensusAnnotations and setup test

    @edmundmiller
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  20. Get custom running

    @edmundmiller
    edmundmiller committed Oct 18, 2024
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  21. Start over

    @edmundmiller
    edmundmiller committed Oct 18, 2024
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  22. refactor: Split into chunks

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Commits on Oct 19, 2024

  1. More tests

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    edmundmiller committed Oct 19, 2024
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Commits on Oct 20, 2024

  1. 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
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