Skip to content

Fix arm64 profile configuration #1630

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
pinin4fjords merged 7 commits into from
Nov 25, 2025
Merged

Fix arm64 profile configuration #1630

pinin4fjords merged 7 commits into from
Nov 25, 2025
+17 −23

Conversation

@pinin4fjords
Copy link
Member

@pinin4fjords pinin4fjords commented Nov 25, 2025 •
edited
Loading

Summary

  • Simplify arm64 profile to use pre-built ARM containers from conf/arm.config instead of requiring Wave
  • Remove incorrect conf/arm.config include from emulate_amd64 profile (emulation uses AMD64 containers)
  • Update documentation to reference arm64 profile instead of arm
  • Fix STAR_ALIGN and STAR_GENOMEGENERATE ARM container references with correct images
  • Remove outdated documentation notes claiming hisat2 and kraken2/bracken are unsupported on ARM (they have containers configured)
  • Add ARM containers for FQ_LINT and UMICOLLAPSE - all open-source modules now have ARM support

Test plan

  • Test pipeline with -profile docker,arm64 on ARM hardware
  • Verify STAR alignment completes successfully with updated containers

🤖 Generated with Claude Code

pinin4fjords and others added 2 commits November 25, 2025 18:09
@pinin4fjords @claude
Fix arm64 profile configuration
6eb995a 
- Simplify arm64 profile to use pre-built ARM containers from conf/arm.config
- Remove Wave dependency from arm64 profile (containers already configured)
- Update documentation to reference arm64 profile instead of arm
- Fix STAR_ALIGN and STAR_GENOMEGENERATE ARM container references
- Remove incorrect arm.config include from emulate_amd64 profile

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords @claude
Add PR #1630 to CHANGELOG
73756c3 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@github-actions
Copy link

github-actions bot commented Nov 25, 2025 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 987608e

+| ✅ 284 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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
  • 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 nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-11-25 20:06:53

pinin4fjords and others added 4 commits November 25, 2025 18:13
@pinin4fjords @claude
Remove outdated ARM limitation notes for hisat2 and kraken2
1a79f0f 
Both hisat2 and kraken2/bracken have ARM containers configured in
conf/arm.config, so the documentation warnings were incorrect.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords
Merge branch 'dev' into fix-arm64-profile
ad7e1e7
@pinin4fjords @claude
Add ARM containers for FQ_LINT and UMICOLLAPSE
0eecbbe 
All open-source modules now have ARM container definitions.
Only Sentieon modules (proprietary) remain without ARM support.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords @claude
Fix FQ_LINT container to use community.wave.seqera.io
817ac88 
🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@pinin4fjords pinin4fjords added this to the 3.22.0 milestone Nov 25, 2025
@pinin4fjords
Copy link
Member Author

pinin4fjords commented Nov 25, 2025

Thanks @mashehu !

@pinin4fjords pinin4fjords merged commit 97dc427 into dev Nov 25, 2025
33 checks passed
@pinin4fjords pinin4fjords deleted the fix-arm64-profile branch November 25, 2025 20:28
@pinin4fjords pinin4fjords mentioned this pull request Nov 26, 2025
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@mashehu mashehu mashehu approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

3.22.0

Development

Successfully merging this pull request may close these issues.

3 participants

@pinin4fjords @mashehu