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Release 2.4 #499

Merged
merged 400 commits into from
Sep 26, 2023
Merged

Release 2.4 #499

merged 400 commits into from
Sep 26, 2023

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jfy133
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@jfy133 jfy133 commented Sep 1, 2023 •
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See changelog: https://github.com/nf-core/mag/blob/dev/CHANGELOG.md#240---2023-09-07

Note large number of files is due to template updates!

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>).
  • 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 May 8, 2023 15:13
@jfy133
Fix channeling with bbnorm
a0933b6
@jfy133
Merge branch 'dev' into run-merging
c6c9730
@jfy133
Apply suggestions from code review
4e0ff55
@jfy133
Revert "Merge branch 'dev' into run-merging"
d8a7573 
This reverts commit c6c9730, reversing
changes made to a0933b6.
@jfy133
Revert "Fix channeling with bbnorm"
aa9c350 
This reverts commit a0933b6.
@jfy133
Merge branch 'run-merging' of https://github.com/jfy133/nf-core-mag i…
7497efd 
…nto run-merging
@jfy133
Update CAT/FASTQ module for latest template compatibility
ed1a451
@jfy133
Fix adapter removal channel
b484874
@prototaxites
Apply suggestions from code review
064bdf1
@prototaxites
Fix nextflow_schema.json
b63854f
@jfy133
Fix GTDB version in consistency
ba802a0
@jfy133
Merge branch 'dev' into fix-gtdbk-version
477cded
@jfy133
Update CHANGELOG.md
8e2e53b
@prototaxites
Update workflow diagram
c668f60
@prototaxites
Add basic binning entry
4161214
@prototaxites
Update docs and add checks
45ad159
@prototaxites
Update changelog
7d1c6e0
@jfy133
Deactivate CONCOCT to make reasonable AWS full test run time
cda7a98
@jfy133
Remove warnings about BUSCO failing to find genes
b3b96c7
@jfy133
Apply suggestions from code review
2c7f437
@jfy133
Update CHANGELOG
7535468
@prototaxites @jfy133
Apply suggestions from code review
0aef6c2 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@prototaxites
Update documentation
f82bfa7
@jfy133
Merge branch 'dev' into multiqc-update
1114e5e
@jfy133
Missing comma
b75b862
@jfy133
Remove unused channel
c9d7b9e
@jfy133
Merge pull request #441 from nf-core/deactivate-full-test-concoct
d10eab0 
Deactivate CONCOCT to make reasonable AWS full test run time
@jfy133
Merge branch 'dev' into busco-warn-removal
ad919cb
@jfy133
Merge pull request #442 from nf-core/busco-warn-removal [skip ci]
9df6b06 
Remove BUSCO warning about no matches found
@jfy133
Refactor MultiQC file passing
d8d511e
ramprasadn
ramprasadn reviewed Sep 7, 2023
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jfy133
jfy133 commented Sep 7, 2023
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Responses from @ramprasadn 's rfist set of comments

CHANGELOG.md Outdated Show resolved Hide resolved
conf/modules.config Outdated Show resolved Hide resolved
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@jfy133 jfy133 mentioned this pull request Sep 15, 2023
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jfy133 commented Sep 15, 2023 •
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@ramprasadn I believe I've addressed all of your comments now, here: #508

I have one more comment from Daniel about updating the URLs in the modules, but hopefully you are happy with everything else!

jfy133 and others added 14 commits September 15, 2023 14:07
@jfy133
Update all URLs and modules except samtools/gtdbtk
e7d9600
@jfy133
Fix porechop and start fixing aDNA samtools faidx fix
6b33f90
@jfy133
Fix aria2 patch
d88cb6e
@jfy133
Fix aria2 patch
62930bd
@jfy133
Merge branch '2.4-review-comments' into registry-update
c5ff72b
@jfy133 @d4straub
Update CHANGELOG.md
f740af7 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
@jfy133
Merge pull request #508 from nf-core/2.4-review-comments
f6cd09f 
2.4 review comments
@jfy133
Merge branch 'dev' into registry-update
3205a96
@jfy133
Fix SAMTools FAIDX
4b15996
@jfy133
Fix ancient DNA samtools FAIX channels and clean up freebayes input c…
6ea1f62 
…hannel code
@jfy133
Fix linting error (not tested!)
b8f07b9
@jfy133
Update CHANGELOG
0a5b517
@jfy133
Merge pull request #509 from nf-core/registry-update
260910d 
[DO NOT MERGE] Registry update for all modules
@jfy133
Update CHANGELOG.md
412a437
ramprasadn
ramprasadn approved these changes Sep 25, 2023
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LGTM! 🚀 🚢

@jfy133
Merge pull request #512 from nf-core/registry-update
3cd985b 
Update CHANGELOG after registry update (missed in previous PR)
d4straub
d4straub approved these changes Sep 26, 2023
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LGTM.

However, the template update came at a bad time...

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jfy133 commented Sep 26, 2023

I am going for a release (merging despite the linting error), and doing an immediate followup release PR with the template

@jfy133 jfy133 merged commit 18a1645 into master Sep 26, 2023
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@d4straub d4straub d4straub approved these changes

@CarsonJM CarsonJM CarsonJM left review comments

@ramprasadn ramprasadn ramprasadn approved these changes

@skrakau skrakau Awaiting requested review from skrakau

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