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Release 2.12.0 #794

Merged
merged 33 commits into from
Nov 15, 2024
Merged

Release 2.12.0 #794

merged 33 commits into from
Nov 15, 2024

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d4straub
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@d4straub d4straub commented Nov 13, 2024 •
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Release 2.12.0

Before being ready for review:

  • Fails unexpected in nf-core linting / nf-core (pull_request) with included_configs: Pipeline config does not include custom configs. Please uncomment the includeConfig line. done
  • AWS full size test manual trigger done
  • manually triggered AWS full size test succeeded done
  • Version update from 2.12.0dev to 2.12.0 done
  • Potentially address phred score mis-detection by dada2 #773 by adding a new parameter postponed

When achieved 2 reviewer approvals, before merging, check if AWS full size test automatically triggered!

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/ampliseq 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).

d4straub and others added 26 commits August 5, 2024 16:00
@d4straub
bump version to 2.12.0dev
524d298
@d4straub
update CHANGELOG
2f7c754
@d4straub
Merge pull request #772 from d4straub/bump-version-2.12.0dev
ba86470 
Bump version 2.12.0dev
@d4straub
merging template updates v3.0.2
fa472fb
@d4straub
fix typo
47efc2f
@nf-core-bot
[automated] Fix code linting
754d92d
@d4straub
update nf-schema and json schemata
68b8731
@d4straub
update md5sums for multiqc files
c9ee1e7
@d4straub
Merge branch 'merging-template-updates_3.0.2' of https://github.com/d…
36e1ef1 
…4straub/ampliseq into merging-template-updates_3.0.2
@d4straub
activate nf-schema lenientMode
4ffc595
@d4straub
fix typo
07fcdd8
@d4straub
update md5sums in snaps
a106c5d
@d4straub
replace https://data.ace.uq.edu.au/public/gtdb/data by https://data.g…
fe2ec7b 
…tdb.ecogenomic.org
@d4straub
update CHANGELOG
e19a70e
@d4straub
remove unused code
d288b34
@d4straub
update test profile snap
1889bab
@d4straub
correct indentation
ce6684f
@d4straub
Merge pull request #785 from d4straub/merging-template-updates_3.0.2
0ac3093 
merging template updates v3.0.2
@d4straub
fix --dada_ref_taxonomy silva=132
12c0370
@d4straub
Merge pull request #786 from d4straub/fix-dada_ref_taxonomy-silva132
f95cf02 
fix --dada_ref_taxonomy silva=132
@d4straub
Remove white spaces in process tags
d8e7eb6
@d4straub
update changelog
08bafc9
@d4straub
Merge pull request #792 from d4straub/rm-white-space-in-process-tag
65bada8 
Remove white space in process tags
@d4straub
update nf-core modules and picrust
4e4c124
@d4straub
update changelog
2c22f74
@d4straub
Merge pull request #793 from d4straub/update-modules-2.12.0dev
9cb08c2 
Update Picrust2 and nf-core modules
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github-actions bot commented Nov 13, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ca63a52

+| ✅ 298 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-14 13:15:57

@d4straub d4straub mentioned this pull request Nov 13, 2024
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@d4straub d4straub changed the title Release 2.12.0 - TEST Release 2.12.0 Nov 14, 2024
@d4straub d4straub marked this pull request as ready for review November 14, 2024 10:49
erikrikarddaniel
erikrikarddaniel approved these changes Nov 14, 2024
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Looks all good to me.

mashehu
mashehu approved these changes Nov 14, 2024
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any ambition on adding the local modules to nf-core/modules?

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afaik this module only helpful for 16S amplicon sequencing, so nothing of broader interest. True for most if not all local modules. So not worth the trouble I think.

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d4straub
d4straub commented Nov 14, 2024
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d4straub
d4straub commented Nov 14, 2024
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@d4straub d4straub merged commit 8f139ce into master Nov 15, 2024
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Thanks for the reviews!

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@mashehu mashehu mashehu approved these changes

@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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