Skip to content

build(arm): drop seqera channel, build SORTMERNA ARM container from bioconda#1854

Merged
pinin4fjords merged 2 commits into
devfrom
sortmerna-bioconda-arm
May 11, 2026
Merged

build(arm): drop seqera channel, build SORTMERNA ARM container from bioconda#1854
pinin4fjords merged 2 commits into
devfrom
sortmerna-bioconda-arm

Conversation

@pinin4fjords
Copy link
Copy Markdown
Member

@pinin4fjords pinin4fjords commented May 11, 2026

Summary

Bioconda now publishes linux-aarch64 builds of sortmerna=4.3.7, so the seqera-channel override in conf/arm.config is no longer required. This switches SORTMERNA to a fresh Wave build off bioconda::sortmerna=4.3.7 and removes the last seqera:: reference in the pipeline.

The legacy STAR 2.6.1d entries that previously also used seqera:: were removed by #1694 when the iGenomes-specific STAR modules were dropped, so SORTMERNA was the last holdout.

Closes #1431.

Changes

  • conf/arm.config: replace SORTMERNA container URLs with a Wave build from bioconda::sortmerna=4.3.7; drop the conda = 'seqera::sortmerna=4.3.7' override and the stale comment pointing at the now-resolved conda-forge pinning issue.

Test plan

  • nf-test ARM test job is green on this PR

🤖 Generated with Claude Code

pinin4fjords and others added 2 commits May 11, 2026 11:20
@pinin4fjords @claude
build(arm): switch SORTMERNA container to bioconda-built Wave image […
4515a80 
…skip ci]

Bioconda now publishes linux-aarch64 builds of sortmerna 4.3.7, so the
seqera-channel override is no longer needed. Replaces the container URLs
with a fresh Wave build off bioconda::sortmerna=4.3.7 and removes the
last seqera:: reference in conf/arm.config (closes #1431).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@pinin4fjords @claude
docs(changelog): link PR #1854 in the SORTMERNA arm.config entry
05c6e4b 
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
@github-actions
Copy link
Copy Markdown

github-actions Bot commented May 11, 2026 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 05c6e4b

+| ✅ 215 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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 base.config: Check the defaults for all processes

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_amd64.config
  • files_exist - File is ignored: conf/containers_conda_lock_files_arm64.config
  • files_exist - File is ignored: conf/containers_docker_amd64.config
  • files_exist - File is ignored: conf/containers_docker_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_https_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_https_arm64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_amd64.config
  • files_exist - File is ignored: conf/containers_singularity_oras_arm64.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • nf_test_content - nf_test_content
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-rnaseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-rnaseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_nf_test - actions_nf_test
  • modules_config - modules_config
  • container_configs - container_configs

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-11 10:24:37

mashehu
mashehu reviewed May 11, 2026
View reviewed changes
Comment thread conf/arm.config
@pinin4fjords
Copy link
Copy Markdown
Member Author

pinin4fjords commented May 11, 2026

Thanks @mashehu !

@pinin4fjords pinin4fjords merged commit 089fb6a into dev May 11, 2026
17 checks passed
@pinin4fjords pinin4fjords deleted the sortmerna-bioconda-arm branch May 11, 2026 11:39
@pinin4fjords pinin4fjords linked an issue May 11, 2026 that may be closed by this pull request
Remove need for use of Seqera conda channels #1431
Closed
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

No milestone

Development

Successfully merging this pull request may close these issues.

Remove need for use of Seqera conda channels

2 participants

@pinin4fjords @mashehu
⚡