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v1.2.3 - Bouncy Basenji Patch PR #583

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v1.2.3 - Bouncy Basenji Patch PR #583

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sofstam
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@sofstam sofstam commented Mar 11, 2025

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/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

sofstam and others added 30 commits January 15, 2025 10:50
@sofstam
Post-release bump version
26e610c
@sofstam
Update CHANGELOG.md
4f49fde
@sofstam
Prettier
2dea5b1
@sofstam
Merge branch 'bump_version_1.3.0' of https://github.com/nf-core/taxpr…
575ef87 
…ofiler into bump_version_1.3.0
@nf-core-bot
[automated] Fix code linting
7f5a785
@sofstam
Merge pull request #568 from nf-core/bump_version_1.3.0
071bcfb 
Post release bump version
@nf-core-bot
Template update for nf-core/tools version 3.1.2
64dcb04
@sofstam
Merge branch 'dev' into nf-core-template-merge-3.1.2
898866f
@sofstam
Update nextflow.config
ac960d4 
Fix is a template change, see nf-core/tools#3416
If your pipeline is affected by this error I think it should be fine to manually apply this patch.
@sofstam @jfy133
Update nextflow.config
a33a73f 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@sofstam
Update zenodo
f2226be
@sofstam
Update nextflow.config
3d54880
@jfy133
Update README.md
8b62db7
@jfy133
Apply suggestions from code review
b8a42de
@sofstam
Merge pull request #569 from nf-core/nf-core-template-merge-3.1.2
34c5079 
Important! Template update for nf-core/tools v3.1.2
@nf-core-bot
Template update for nf-core/tools version 3.2.0
622585a
@sofstam
Merge branch 'dev' into nf-core-template-merge-3.2.0
b524cb0
@jfy133
Merge pull request #571 from nf-core/nf-core-template-merge-3.2.0
f11fd27 
Important! Template update for nf-core/tools v3.2.0
@jfy133
Improve docs for taxpasta related flags
22380d6
@jfy133
Merge pull request #573 from nf-core/better-docs
7415c81 
Better docs for taxpasta related flags
@jfy133
Update CHANGELOG.md
ec1ac99
@muniheart
Include batch index in task label.
c802f6f
@muniheart
Fix: Use db_name in process tag.
84b4b9c
@muniheart
Sort input channel to krakenuniq to enable task caching.
e981c70 
Sort the input channel to ensure batches of input will remain constant across runs.
@muniheart
Replace collect() with toSortedList()
6f7506a 
As suggested by @Midnighter, using toSortedList in place of collect improves clarity.

Also: [ suggested by @Midnighter ]
Remove closure argument to flatMap.  The operator with closure argument performed the default behavior of the operator without closure.
@muniheart
Update CHANGELOG.md
9c697c5
@muniheart
Update CHANGELOG.md
7500711
@jfy133
Merge pull request #575 from nf-core/changelog-for-docschagnes
c3a6b58 
Changelog for for #573
@jfy133
Merge branch 'dev' into master
184d1f8
@muniheart
Changed sort comparator to avoid type mismatch error.
cb510bd 
A samplesheet with both integer and non-numeric ( string ) values of sample caused type-mismatch error when compared.  Generate prefix string from meta and compare on prefix.
muniheart and others added 18 commits February 12, 2025 20:15
@muniheart
Fixed: Reinsert deleted arguments to closure.
382c4b3
@jfy133
Satisfy linting
c7c98e4
@mashehu
Fix keyword in nextflow_schema.json
4484e71
@mashehu
update changelog
612a94c
@mashehu
Merge pull request #578 from nf-core/fix-schema-keyword
24933cc 
Fix keyword in nextflow_schema.json
@muniheart
Adjust list indices.
c2a907b
@muniheart
Moved sort operation.
a2705e1 
Sorting within each group produced by groupTuple is sufficient to ensure the batches will remain the same, regardless of the order of the input channel.  Position the sort after input channel has been grouped, and after prefix has been defined.  Sort by prefix, guaranteed to be distinct within each group, to preserve order across workflow runs.
@mashehu
remove links to multiqc plots
ac4e54f 
took me a bit to figure out that it wasn't actually problematic website rendering that didn't render the images 😁 

Probably a merge artifact from a template update?
@jfy133
Merge pull request #579 from nf-core/remove-links-multiqc-plot
593aba1 
Remove links to multiqc plots
@AlexHoratio
analysis_read_reads -> analysis_ready_reads
e61d649
@AlexHoratio
space after full stop
e3e680a
@AlexHoratio
not can -> nor can
595ae3d
@AlexHoratio
added me to README.md
f4f4b33
@jfy133
Merge pull request #580 from AlexHoratio/minor_typos_fix
220f2c7 
Minor typo fixes
@jfy133
Merge pull request #576 from muniheart/master
3c82ed6 
Sort input to krakenuniq to enable retrieval of cached batch runs. #570
@jfy133
Add missing template updates
07cbf7f
@jfy133
add missing typo fixes
919dbfd
@sofstam
Merge pull request #582 from nf-core/changelog-post3.20t-tools
5db1dc1 
Changelog post-3.1.2 and 3.2.0 template updates
@jfy133
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jfy133 commented Mar 11, 2025

Forgot version bump I think @sofstam 😬

@sofstam
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sofstam commented Mar 11, 2025

I realized it a bit late but I am updating the PR :)

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github-actions bot commented Mar 11, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 48d4070

+| ✅ 280 tests passed       |+
!| ❗  18 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • local_component_structure - krona_cleanup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - kraken2_standard_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - standardisation_profiles.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - visualization_krona.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - nonpareil.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-11 14:36:28

erikrikarddaniel
erikrikarddaniel approved these changes Mar 11, 2025
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LGTM.

@sofstam
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sofstam commented Mar 11, 2025

#584

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@sofstam @jfy133 @erikrikarddaniel @nf-core-bot @muniheart @mashehu @AlexHoratio