add ARM CI test #1641
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add ARM CI test #1641
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mashehu
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@mashehu thanks for setting this up, it flagged a bunch of stuff I hadn't noticed from manual ARM trials in AWS. I think I'm going to need a patch release! Pushed fixes for ARM CI: 1. Add SKIP_SENTIEON support
2. Container updates
3. Test/snapshot updates
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- Add SKIP_SENTIEON environment variable support to nf-test.config for ARM runners and fork CI runs where Sentieon is unavailable - Split Sentieon tests into separate files (main.sentieon.nf.test) for selective exclusion via nf-test ignore patterns - Update CI workflows to set SKIP_SENTIEON on ARM and forks 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Update STAR igenomes modules to Wave containers with samtools 1.21 for consistent versions across x86 and ARM architectures - Add ARM container selectors for STAR_ALIGN_IGENOMES and STAR_GENOMEGENERATE_IGENOMES modules - Update DESEQ2_QC container configuration for ARM support - Update arm.config with ARM-compatible container mappings 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
- Remove hardcoded --platform=linux/amd64 from test nextflow configs - Update DESEQ2_QC tests for ARM architecture compatibility - Update test snapshots for new container versions (samtools 1.21) - Fix arriba test to snapshot BAM filename only to avoid architecture-specific content differences - Remove sentieon test entries from main snapshot files (now in separate main.sentieon.nf.test.snap files) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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pinin4fjords
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Nov 27, 2025
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Linking back that we specifically decided against doing this Happy to have the philosophy updated, but we should obviously document this somewhere. |
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This runs for now the same tests as the normal CI. If we want we could just run a subset (by adding a tag to the tests, like we do with gpu testing for example in methylseq)