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nf-core/mag 3.2.0 release PR #699

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nf-core/mag 3.2.0 release PR #699

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@jfy133 jfy133 commented Oct 22, 2024

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/mag 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).

jfy133 and others added 30 commits September 9, 2024 16:08
@jfy133
Replace local spades modules with official nf-core version (missing f…
7d3650e 
…ix CPU trick)
@jfy133
Update CHANGELOG.md
391ebd4
@jfy133
Fix output docs
e6301c8
@jfy133
Make sure warnings log also gets a prefix
debd080
@jfy133
Merge branch 'dev' into bump-metaspades
89f98e2
@jfy133
Fix a syntax error (Ben made me do it)
4d19b8f
Added modules porechop/abi and chopper for QC of long reads
08445cf
Move long read preprocessing into subworkflow, and swapping porechop …
5aa3049 
…module to porechop/abi
Remove module import from main workflow, and add PORECHOP_ABI in conf…
451612a 
…/modules.config
@jfy133
Switch local MEGAHIT to official nf-core one
5437376
@jfy133
Fix wrongly set branch
12b13d3
@jfy133
Merge branch 'dev' into bump-metaspades
830a66e
@jfy133
Fix linting
7d7ad71
@muabnezor
Exchange local filtlong module to nf-core/filtlong
59ef702
@muabnezor
Add filtlong and porechop logs to multiqc
cd5ce2f
@muabnezor
Added --longread_preprocessing_tools parameters, to let user specify …
5820fb4 
…long read preprocessing tools. Currently only has the option to specify porechop_abi, but I decided this is a nice solution for future tools that the user might want to chose among
@muabnezor
Merge branch 'dev' into move_lr_qc
5335fc5
@muabnezor
Update modules/nf-core/filtlong/main.nf
1496ce9 
Fix linting problem
@muabnezor
make subworkflow name more verbose
c11601a
@muabnezor
make --longread_adaptertrimming_tool as enum porechop or porechop_abi
31deb5c
@muabnezor
Make prefix for porechop/porechop-abi more verbose
b2da50b
@muabnezor
lint
8955e31
@muabnezor
Change default search pattern for filtlong.log files for the filtlong…
644e2b1 
…module in multiqc
@muabnezor @jfy133
Update CHANGELOG.md
3e15502 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@muabnezor @jfy133
Update CHANGELOG.md
ec8538c 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@muabnezor @jfy133
Update nextflow_schema.json
c6fb9b3 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@muabnezor @jfy133
Update conf/modules.config
b24f52f 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@muabnezor @jfy133
Update conf/modules.config
fcf509c 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@muabnezor @jfy133
Update conf/modules.config
8f9cac6 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@muabnezor @jfy133
Update nextflow_schema.json
10ecdc5 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
d4straub
d4straub reviewed Oct 22, 2024
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d4straub
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d4straub
d4straub approved these changes Oct 22, 2024
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Looks good to me once the test are passing ;)

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@maxulysse
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I think you can disable conda tests for the pipeline for now

@jfy133
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jfy133 commented Oct 22, 2024

I think you can disable conda tests for the pipeline for now

I don't think so, it should work. I think it's a badly pinned environmental yml against the mulled container that it was built with. It should be easy enough fix, o suspect

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jfy133 commented Oct 24, 2024

See @maxulysse ! I'm a conda wizard!

(I think it was acutally because the module had anaconda:: as a chanel specified for one the packages... 😱 )

jannikseidelQBiC
jannikseidelQBiC approved these changes Oct 25, 2024
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LGTM! Only one tiny thing caught my eye ;) When the comments of @d4straub are addresses you are good to go, imo.

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jfy133 commented Oct 25, 2024

@nf-core-bot fix linting

jfy133
jfy133 commented Oct 26, 2024
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jfy133 commented Oct 26, 2024
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jfy133 and others added 2 commits October 26, 2024 15:21
@jfy133
Update workflows/mag.nf
feeb14a
@jfy133 @d4straub
Update .nf-core.yml
2963ba0 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@jfy133 jfy133 mentioned this pull request Oct 26, 2024
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@d4straub d4straub d4straub approved these changes

@jannikseidelQBiC jannikseidelQBiC jannikseidelQBiC approved these changes

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@jfy133 @maxulysse @d4straub @jannikseidelQBiC @muabnezor @nf-core-bot