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Try matthias' fix to download #1439

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Try matthias' fix to download #1439

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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/rnaseq 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 October 16, 2024 14:44
@maxulysse
Merge pull request #1417 from nf-core/master
e9fa18c 
Update dev from master
@pinin4fjords
Bump versions back to 3.17.0 after release
dca14c5
@pinin4fjords
Update CHANGELOG
4336b2b
@pinin4fjords
Prettier
f919609
@pinin4fjords
Merge pull request #1418 from nf-core/postrelease_3.16.1
5f2badc 
Bump versions back to 3.17.0 after release
@pabloaledo
appy changes for ARM
d59ecf7 
Signed-off-by: Pablo <[email protected]>
@pinin4fjords
Merge branch 'arm_3.16.1' into dev
991637c
@pinin4fjords
Fix up config
4bdae48
@pinin4fjords
Reset environment ymls
c9d616b
@pinin4fjords
Reset main.nfs with software changes only
9f640ab
@pinin4fjords
Link sw configs to arm profile
00cff4c
@pinin4fjords
Add process block
f281e0b
@pinin4fjords
note pins
f5208dd
@pinin4fjords
Remove conda overrides that were having no impact
ea8b9e8
@pinin4fjords
Use different RSEQC pin
db02d99
@pinin4fjords
update BEDGRAPHTOBIGWIG pin
4a8ed2b
@pinin4fjords
Fix annotation
b86a6f9
@pinin4fjords
Don't think we need the RSEQC pin
1b96eb8
@pinin4fjords
correct ucsc
4e5d7a3
@pabloaledo
Merge pull request #1 from pinin4fjords/sw_to_conf
bbd3452 
Sw to conf
@pinin4fjords
Triage arm deps
902367e
@pinin4fjords
Non-igenomes STAR can use the latest star
328d02d
@pinin4fjords
remove rogue comment
2f92bfc
@pinin4fjords
update arm conf
0a563dc
@pinin4fjords
Bump lots of modules so that conda versions have arm builds
8a3b58f
@pinin4fjords
Update prepare_genome snaps
6739fbd
@pinin4fjords
Update align_star snaps
75fad6f
@pinin4fjords
Update quantify_rsem snaps
a036f5d
@pinin4fjords
[skip ci] First batch of pipeline test updates
5dd65b9
@pinin4fjords
[skip ci] Update subworkflow snaps due to patch on module
7568b2d
pinin4fjords and others added 27 commits October 23, 2024 10:36
@pinin4fjords
[skip ci] Reorg ARM bits
896dd74
@drpatelh
Update arm.config
314ea85
@pinin4fjords
Fix syntax error
251481f
@pinin4fjords
Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1
cde5fef
@pinin4fjords
revert trimgalore tweak to appease linter
f59132a
@pinin4fjords
Update pipeline-level tests
40f05c5
@pinin4fjords
Merge branch 'arm_3.16.1' of https://github.com/nf-core/rnaseq into a…
2156f5d 
…rm_3.16.1
@pinin4fjords
Update CHANGELOG
79370d3
@pinin4fjords
Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1
424137a
@pinin4fjords
Merge pull request #1425 from nf-core/arm_3.16.1
fb057c9 
Add profile for ARM compatibility
@pinin4fjords
Bump versions
9b9181c
@pinin4fjords
update changelog
62f4ffe
@pinin4fjords
Merge pull request #1432 from nf-core/prerelease_3.17.0
facaabd 
Bump versions for 3.17.0 release
@maxulysse
update CHANGELOG
2a50999
@maxulysse
update and patch modules
4316615
@maxulysse
Merge pull request #1434 from maxulysse/default_registry_no_exception
434f0b7 
No exception for default registry
@maxulysse
update CHANGELOG
e94558b
@maxulysse
fix CI
b5f530f
@maxulysse
Merge branch 'dev' into CHANGELOG
f389d0f
@maxulysse
update CHANGELOG
97d3697
@maxulysse
fix GHA
23d3ee7
@maxulysse
revert GHA
b55c81a
@maxulysse
revert CHANGELOG
9690d29
@maxulysse
update CHANGELOG
ac1b7e0
@maxulysse
remove conda from matrix
3890344
@pinin4fjords
Merge pull request #1437 from maxulysse/CHANGELOG
1c5d267 
update CHANGELOG
@pinin4fjords
Update download_pipeline.yml
a75ee7f
@github-actions GitHub Actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@pinin4fjords pinin4fjords marked this pull request as draft October 23, 2024 21:56
@github-actions GitHub Actions
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github-actions bot commented Oct 23, 2024 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a75ee7f

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-23 21:58:08

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4 participants
@pinin4fjords @maxulysse @pabloaledo @drpatelh