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fix: regenerate .fai index before reading and guard empty edx samples Deploy Documentation #24: Commit 43ef7cd pushed by jayhesselberth
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docs: sync mermaid pipeline diagrams between README and docs/index Deploy Documentation #23: Commit 1f46c8d pushed by jayhesselberth
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chore: migrate documentation from mkdocs to zensical Deploy Documentation #22: Commit 1efe49a pushed by jayhesselberth
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feat: move EDX demultiplexing before alignment (#88) Deploy Documentation #21: Commit 56a1bbe pushed by jayhesselberth
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docs: document dual barcoding (WDX + EDX) support Deploy Documentation #20: Commit 20b47f7 pushed by jayhesselberth
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chore: upgrade basecalling model to v5.3.0, add dorado version check Deploy Documentation #19: Commit ef1e765 pushed by jayhesselberth
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chore: upgrade dorado to 1.4.0, pin modkit >=0.6.1, single source of … Deploy Documentation #18: Commit c2da79e pushed by jayhesselberth
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docs: document WarpDemuX adapter sets, naming convention, and upstrea… Deploy Documentation #17: Commit b5beac5 pushed by jayhesselberth
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feat: consolidate demux env into default and add edx concordance Deploy Documentation #16: Commit 7acfbbc pushed by jayhesselberth
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docs: update CHANGELOG, rules, and output docs for v0.1.1 Deploy Documentation #15: Commit 7d651c9 pushed by jayhesselberth
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docs: document squiggy-session.json across all docs Deploy Documentation #14: Commit 8c0a805 pushed by jayhesselberth
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feat: eliminate merge_pods_for_demux from WarpDemuX workflow Deploy Documentation #13: Commit 36fe28f pushed by jayhesselberth
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docs: update documentation for v1.3.1 release Deploy Documentation #12: Commit 60a9784 pushed by jayhesselberth
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feat: add native SLURM cluster support Deploy Documentation #11: Commit b5e0da6 pushed by jayhesselberth
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fix: resolve GLIBCXX version errors with configurable CUDA support Deploy Documentation #10: Commit be3ed23 pushed by jayhesselberth
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docs: add citation for White et al. 2025 Nat Commun Deploy Documentation #9: Commit f2cfdc7 pushed by jayhesselberth
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fix: auto-install WarpDemuX on demux environment activation Deploy Documentation #8: Commit fb764b7 pushed by jayhesselberth
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docs: add pixi installation instructions Deploy Documentation #7: Commit 9408fba pushed by jayhesselberth
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fix: enable emoji extension for Material icons in mkdocs Deploy Documentation #6: Commit 56b4b9a pushed by jayhesselberth
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feat: add tRNA reference validation and building step (#78) Deploy Documentation #5: Commit 534f0c6 pushed by jayhesselberth
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docs: move navigation from top tabs to left sidebar Deploy Documentation #4: Commit 56a7dd0 pushed by jayhesselberth
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docs: add comprehensive MkDocs documentation website (#77) Deploy Documentation #3: Commit ac50971 pushed by jayhesselberth
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fix: correct pymdownx.highlight config options Deploy Documentation #2: Commit c2cf4b9 pushed by jayhesselberth
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docs: add comprehensive MkDocs documentation website Deploy Documentation #1: Commit 6496235 pushed by jayhesselberth
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