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Fake release to fix sync and all nf-core goodness#122

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maxulysse wants to merge 37 commits into
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Fake release to fix sync and all nf-core goodness#122
maxulysse wants to merge 37 commits into
mainfrom
dev

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@maxulysse

@maxulysse maxulysse commented Jul 14, 2025

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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/references 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).

maxulysse and others added 30 commits January 8, 2025 10:53
@maxulysse
Compress vcf when not compressed already (#72)
5a5059a 
* update CHANGELOG

* fix PR number
@maxulysse
Update modules (#73)
c2f1d3d 
* update modules

* restore patch

* update snapshots

* update subworkflow

* update CHANGELOG

* update snapshot
@maxulysse
Add DOI and back to dev (#74)
7de0e97 
* update doi

* Update CHANGELOG and snapshots

* Apply suggestions from code review

* Apply suggestions from code review

* newline
@maxulysse @heuermh
Template update for nf-core/tools version 3.1.1 (#75)
bf51f05 
* Template update for nf-core/tools version 3.1.1

* master -> main

* fix linting

* Apply suggestions from code review

* update ro-crate

* update workflow

* keep nextflow 24.10.1

* ignore snapshots in editor config

* Apply suggestions from code review

* lint

* keep same depth

* Apply suggestions from code review

* code polish

* restore main.nf

* Apply suggestions from code review

* polish

* Apply suggestions from code review

* polish

* Update nextflow.config

* Update main.nf

* Update nextflow.config

* update CHANGELOG

* Apply suggestions from code review

Co-authored-by: Michael L Heuer <heuermh@acm.org>

* master/main -> main

---------

Co-authored-by: Michael L Heuer <heuermh@acm.org>
@maxulysse
Add more extraction for sarek related test files (#76)
4f03a91 
* no need for this file

* new modules

* add more extract for sarek test files

* update CHANGELOG
@maxulysse
FIX: createsequencedictionary creation (#77)
8112ae8
@maxulysse
rename input to asset + docs (#78)
6bc916e 
* rename input to asset

* update CHANGELOG

* fix linting

* fix comments
@maxulysse
Improving vcf handling (#79)
2327364 
* trying out flat structure for vcf related files

* this is the nested structure I'd like

* proper flat structure

* fix syntax

* code polish

* order

* 2.3.0 is not working with output

* no doom

* nested

* refactor and update tests

* array

* glob

* transpose vcf to handle multiple vcf with globs
@maxulysse
Improve sarek vcf handling (#80)
c336b1d 
* CHANGELOG update

* handle multiple vcf

* CHANGELOG.md update

* restore comments

* update sarek test and use asset file from references-asset
@maxulysse
Fix un-necessary fasta_fai re-generation (#81)
842c70d 
* CHANGELOG update

* handle multiple vcf

* CHANGELOG.md update

* restore comments

* update sarek test and use asset file from references-asset

* more tests

* do not regenerate fai if not needed

* update CHANGELOG
@maxulysse
use schema from utils_references (#84)
c8a1e0a 
* use schema from utils_references

* fix paths

* Apply suggestions from code review

* fix assets

* fix bash shell issues

* not keeping the s3 files for now
@maxulysse
implement automatic sharding for nf-test (#87)
e7adcc0 
* implement automatic sharding for nf-test

* fix template
@maxulysse
Important! Template update for nf-core/tools v3.2.0 (#86)
b4bfa91 
* Template update for nf-core/tools version 3.1.1

* Template update for nf-core/tools version 3.2.0

* Apply suggestions from code review

* fix rocrate

* fix linting

* fix more linting

* fix master -> main

* update CHANGELOG

* fix sharding

* fix tests
@maxulysse
Update all modules (#88)
c0dcb06 
* update CHANGELOG

* nf-core modules update -f -a
@maxulysse
Fix links (#90)
991bff2 
* Fix links

* Update CHANGELOG.md
@maxulysse
update pipelines with new ontologies and update rocrate (#89)
fa183b9
@maxulysse
Split up references generation into separate subworkflows based on dn…
b2bfbb7 
…aseq or rnaseq (#91)

* began refactor

* rename tests

* continue names update

* Apply suggestions from code review

* regenerate all tests

* improve extract

* rename

* reuse closure

* code polish + better comments

* minor polish

* move out YAML_TO_CHANNEL + EXTRACT

* refactor generation by pipeline

* rescue EXTRACT_ARCHIVE versions

* ALPHABETICAL ORDER

* rescue sizes and faidx

* rescue sizes execution

* reorder snapshot

* restore comments

* uncomment

* update CHANGELOG

* rescue intervals generation

* typo

* no need for empty channel

* reorganize config to prepare moving subworkflows to modules

* simplify further extract subworkflow
@maxulysse
Improve prepare_genome usage and add tests (#92)
848d44d 
* remove forgotten subworkflow

* add tests

* string() just to be safe

* update tests

* should fix tests

* fix new tests

* improve rnaseq usage

* regenerate tests

* add more tests

* reorder snapshot

* better and prettier snapshots
@maxulysse
refactor meta usage (#93)
9a046f3 
* refactor meta usage

* safer join

* regenerate snapshots

* nf-core modules patch

* remove unstable files from snapshots

* closure 🚀

* join_by_id -> join_by_meta_id
@maxulysse
Update action.yml (#94)
9baeb6c
@maxulysse
Update nf-test actions (#95)
fb0f50f 
* Update action.yml

* Update action.yml
@maxulysse
Update nf-core modules and subworkflows (#96)
2f5dff9 
* rename subworkflow

* better comments

* use nf-core version of subworkflow

* update all modules

* update provenance

* fix gffread usage

* update CHANGELOG

* fix build_intervals usage

* fix memory requirements for test for BWAMEM2_INDEX
@maxulysse
better comments on the GHAs (#97)
1e265f3 
* better comments

* polish to trigger tests

* Update action.yml

* Update nf-test.yml
@maxulysse
rename test file (#105)
75527e8
@maxulysse
Improve CI (#109)
94e9fd2 
* early fail

* update CHANGELOG

* fix name of confirm-pass
@maxulysse
Install modules and create subworkflows from nf-side (#110)
e87feb5 
* main.nf

* install prepare_genome_dnaseq prepare_genome_rnaseq

* update bowtie

* update prepare_genome_dnaseq

* update snapshots

* fix config issues

* typo

* update prepare_genome_rnaseq
@maxulysse
rename and improve (#112)
91f98d1
@maxulysse
Fix paths (#113)
7750e18 
* fix path to files

* fix snapshots

* source datasheets are in nf-core/references-datasheets

* fix paths

* fix path to test files

* fix path to test input

* update createsequencedictionay

* update samtools tests

* update tests and snapshots

* fix path and update snapshots

* fix path and update snapshots

* fix path and update snapshots

* use test input without gtf

* fix snapshots

* update snapshots
@maxulysse
Improve schema and usage of the utils_reference subworkflow (#111)
8cc736e 
* update CHANGELOG

* update all modules

* update schema

* fix schema

* use subworkflow

* new params references_basepath

* be consistent about params
@maxulysse
Important! Template update for nf-core/tools v3.2.1 (#115)
c95e80f 
* Template update for nf-core/tools version 3.1.1

* Template update for nf-core/tools version 3.2.0

* Template update for nf-core/tools version 3.2.1

* Apply suggestions from code review

* fix merge conflicts

* Update subworkflows/local/utils_nfcore_references_pipeline/main.nf
maxulysse and others added 3 commits May 22, 2025 15:49
@maxulysse
add metro map and update docs and citations (#118)
b0601c8 
* add metro map and update docs

* Update README.md

* update CHANGELOG

* 30° angles instead of 45° and more spacing

* improve comments

* add contributor

* typo

* Add links to tools

* update CITATIONS
@maxulysse
Add logo (#119)
527f23b 
* add logo

* update map and logo

* update logo

* export page

* export page
@maxulysse @nvnieuwk
Important! Template update for nf-core/tools v3.3.2 (#121)
14d487f 
* Template update for nf-core/tools version 3.1.1

* Template update for nf-core/tools version 3.2.0

* Template update for nf-core/tools version 3.2.1

* update workflow output defs

* update ci nextflow version

* lint

* Template update for nf-core/tools version 3.3.2

* update changelog

* typo

* fix publishing

* fix snapshot

* simpligy publishing

* update paths and snapshots

* fix merge

* update CHANGELOG

* fix snapshots

---------

Co-authored-by: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
@maxulysse maxulysse changed the title Fix main Fake release to fix sync and all nf-core goodness Jul 14, 2025
maxulysse added 4 commits July 14, 2025 19:51
@maxulysse
Prepare rc 0 2 (#123)
22de15c 
* bump version

* Trigger Build

* Update CHANGELOG.md

* unstable on conda

* fix gitignore
@maxulysse
update all modules (#124)
b497e20 
* update all modules

* update sarek references

* fix linting
@maxulysse
use nf-core-utils and topics and update all modules/subworkflows (#125)
14c4b68
@maxulysse
restore path to publish folders (#127)
2cdaeac 
* restore path to publish folders

* update nftignore

* update snapshots and nftignore

* fix snapshots

* fixing refseq.bin

* forgot wbcel235
@mashehu

mashehu commented Oct 2, 2025

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why is this needed?

@maxulysse

maxulysse commented Oct 23, 2025

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We believed with Julia that it was needed because I never got the template sync until now

@maxulysse maxulysse closed this Oct 23, 2025
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2 participants

@maxulysse @mashehu