refactor: code quality improvements from PR #1717 review#1735
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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 #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 #1730. Addresses review feedback from @adamrtalbot in PR #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>
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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. |
2 tasks
adamrtalbot
approved these changes
Feb 27, 2026
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
GPU runners are expensive - just test minimum version. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
|
mashehu
reviewed
Feb 27, 2026
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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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):NXF_VERenv var (overridden by job-level matrix)Test plan
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