refactor: code quality improvements from PR #1717 review#1733
Closed
pinin4fjords wants to merge 5 commits into
Closed
refactor: code quality improvements from PR #1717 review#1733pinin4fjords wants to merge 5 commits into
pinin4fjords wants to merge 5 commits into
Conversation
Replace `{ tuple -> tuple[1] }` and similar patterns with named
destructuring (e.g. `{ _meta, stats -> stats }`) throughout the
main workflow for improved readability.
Also rename `ch_dummy_file` to `ch_transcript_fasta_placeholder`
to clarify its purpose as a placeholder input for quantification
subworkflows.
Addresses review feedback from @adamrtalbot in PR nf-core#1717.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Remove redundant workflow-level NXF_VER env var (overridden by matrix-level NXF_VER at the job level) - Add latest-everything to NXF version matrix, matching nf-test.yml and nf-test-arm.yml - Add continue-on-error for latest-everything and report step to match other CI workflows Note: NXF version bump from 25.04.0 to 25.04.3 is handled separately in PR nf-core#1730. Addresses review feedback from @adamrtalbot in PR nf-core#1717. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Nextflow 25.04.0 passes the obsolete `--mkdir` flag to `conda create`, which fails with recent conda versions. Fixed in nextflow-io/nextflow#5947. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Member
|
Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Member
Author
|
Closing - will re-create from the main repo instead of fork. |
mashehu
reviewed
Feb 27, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Addresses code quality feedback from @adamrtalbot's PR #1717 review:
{ tuple -> tuple[1] }patterns with named destructuring ({ _meta, stats -> stats }) throughoutworkflows/rnaseq/main.nffor improved readabilitych_dummy_filetoch_transcript_fasta_placeholderto clarify its purposeassets/METRO_MAP.mdtodocs/dev/metro_map.mdnf-test-gpu.yml) with other CI workflows:NXF_VERenv var (overridden by job-level matrix)latest-everythingto NXF version matrixcontinue-on-errorand report step forlatest-everythingAlso cherry-picks PR #1730 (Nextflow 25.04.3 bump) to avoid conflicts.
Test plan
🤖 Generated with Claude Code