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Performing merge for first release #25

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Performing merge for first release #25

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atrull314
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@atrull314 atrull314 commented Jul 12, 2024 •
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/scnanoseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

lianov and others added 30 commits August 24, 2023 14:24
@lianov
removed hardcoded isoquant version and debug code
adda109
@lianov
added stranded param to isoquant
a159f6f
@lianov
added knee plot to results, isoquant version to ch_versions, cleaned …
188ee95 
…comment
@atrull314
First pass at module updates
a70b5a6
@atrull314
Merge branch 'isoquant_dev' of https://github.com/U-BDS/scnanoseq int…
adb0208 
…o isoquant_dev
@atrull314
Removing debug print
e63c1df
@atrull314
Fixing syntax in modules.conf for base modules
643a372
@atrull314
Adding the ability to merge replicates
f15260e
@atrull314
Reducing requirements for minimap2_index
fd95b1c
@atrull314
Template update for nf-core/tools version 2.9
130217a
@atrull314
Updating nf-core template
e48b020
@atrull314
Merge pull request #5 from U-BDS/isoquant_dev
316136c
@atrull314
Removing enable_conda from local modules and updating modules in orde…
e62bc27 
…r to resolve linting issues
@atrull314
Tweaking version to see if that resolves linting error
02eed9d
@atrull314
Changing outdirs for minimap bams
e58f12a
@atrull314
Fixing issues with multiqc introduced by template updates
ee196a7
@atrull314
Updating BLAZE scripts
25e3301
@atrull314
Removing hardcoded cpus in BLAZE config
71cb5a0
@atrull314
Changing preextract fastq to take in zip files
1d7464d
@lianov
tool versioning updates
9b2f33a
@lianov
removing depracated module and minor clean-ups
4b8ae45
@lianov
added minimal test config
4643910
@lianov
close issue #4
a33a43b
@lianov
fixing issue with channels for preextract zip file
fb36eb8
@atrull314
Rewriting modules config
75197d1
@atrull314
Correcting issues in workflow so that it passes zipped fastqs around …
70eaa51 
…regardless of if the user chooses to trim files or not
@atrull314
Correcting processes that show up as 'no matching config selector'
1071e0a
@atrull314
Removing unused module imports
c336588
@atrull314
Further cleanup of modules config
f527735
@atrull314
Fixing PREPARE_GTF missing selector warning
9fb8c38
@atrull314
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Hi @mashehu -- Just wanted to ping for the above questions to make sure we aren't missing anything.

Also just wanted to confirm, do we need an additional review for the first release?

LilyAnderssonLee
LilyAnderssonLee reviewed Sep 6, 2024
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@LilyAnderssonLee LilyAnderssonLee left a comment

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Very nice work! I just have a few small comments.

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atrull314 and others added 12 commits September 11, 2024 15:31
@atrull314 @LilyAnderssonLee
Updating based on PR suggestions from LilyAnderssonLee
09cc318 
Co-authored-by: Lili Andersson-Li <[email protected]>
@atrull314 @LilyAnderssonLee
Updating based on PR suggestions from LilyAnderssonLee
e3fdad9 
Co-authored-by: Lili Andersson-Li <[email protected]>
@atrull314 @LilyAnderssonLee
Updating based on PR suggestions from LilyAnderssonLee
e373c33 
Co-authored-by: Lili Andersson-Li <[email protected]>
@atrull314 @LilyAnderssonLee
Updating based on PR suggestions from LilyAnderssonLee
28bd9ec 
Co-authored-by: Lili Andersson-Li <[email protected]>
@atrull314 @LilyAnderssonLee
Updating based on PR suggestions from LilyAnderssonLee
4333dca 
Co-authored-by: Lili Andersson-Li <[email protected]>
@atrull314 @LilyAnderssonLee
Updating based on PR suggestions from LilyAnderssonLee
17c5dcd 
Co-authored-by: Lili Andersson-Li <[email protected]>
@atrull314 @LilyAnderssonLee
Update README.mdUpdating based on PR suggestions from LilyAnderssonLee
9136b5c 
Co-authored-by: Lili Andersson-Li <[email protected]>
@atrull314 @LilyAnderssonLee
Updating based on PR suggestions from LilyAnderssonLee
a516717 
Co-authored-by: Lili Andersson-Li <[email protected]>
@atrull314
Fixing linting in README
0b8232f
@atrull314
Adding light logo to linting ignore
b6c3866
@atrull314
Removing need for dummy file to samtools_view
ae824cd
@atrull314
Fixing changelog; Adding TBD for date
0033a1c
@lianov lianov requested a review from mashehu September 13, 2024 15:27
@atrull314
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Hi @LilyAnderssonLee,

Thank you for the review! I believe I've managed to resolve most of your suggestions -- with the exception of one question back. Please let me know if there's any other questions.

Thanks!

LilyAnderssonLee
LilyAnderssonLee reviewed Sep 24, 2024
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Hi @LilyAnderssonLee and @mashehu,

I believe we've got all points resolved with some last couple of questions for @mashehu on the other PR, please let us know if you see anything else!

Thanks,
Austyn

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@lianov lianov lianov left review comments

@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

@mashehu mashehu Awaiting requested review from mashehu

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6 participants
@atrull314 @mashehu @lianov @LilyAnderssonLee @Salome-Brunon @nf-core-bot