refactor: remove the unused leviosam2 chain-lift rules - #70
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This was referenced Aug 14, 2026
Nothing consumes the leviosam2 outputs, chain mode has been broken since the fire rule stopped producing a bam (its input referenced a bam output that no longer exists), and the rules carried further latent bugs (index written to a hardcoded shared path instead of the declared output). Delete the rules and the chain/levio_exe config options. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Part 2 of a 3-PR stack (#69 → this → #68). Merge after #69; the base retargets to main automatically when #69 merges.
Nothing consumes the leviosam2 outputs (
rule allnever references them), chain mode has been broken sincerule fireswitched to CRAM output (the levio input referencedrules.fire.output.bam, which no longer exists, making anychain:config a parse-time error), and the rules carried further latent bugs (the index was written to a hardcoded shared path rather than its declared per-sample output). A single globalchain:also cannot coexist with the per-sample references arriving in #68. This removesworkflow/rules/levio.smkand thechain/levio_execonfig options.🤖 Generated with Claude Code