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rob-pclaude
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Fix flex-quant: use piscem map-sc subcommand (not map-scrna)
The released C++ piscem (bioconda) uses 'map-sc' as the single-cell mapping subcommand. 'map-scrna' is only available in the Rust piscem-rs development build. This caused flex-quant to fail with "unrecognized subcommand 'map-scrna'" for users with the released piscem. Fixes #191. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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src/simpleaf_commands/flex_quant.rs

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -192,7 +192,7 @@ pub fn flex_map_and_quant(af_home: &Path, opts: FlexQuantOpts) -> anyhow::Result
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info!("Mapping reads with piscem...");
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let mut piscem_cmd = std::process::Command::new(&piscem_info.exe_path);
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piscem_cmd
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.arg("map-scrna")
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.arg("map-sc")
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.arg("-i").arg(&index_path)
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.arg("-g").arg(chem.geometry())
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.arg("-o").arg(&map_output)

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