V0.7.1 - #30
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poojachandra
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Sep 4, 2026
poojachandra
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- Output all candidate solutions, not just the optimal one
- Align each solution's params.txt Log-likelihood with its own result
Bases this branch on full-results (v0.6.0), which already includes outputting all candidate solutions instead of just the optimal one. - Replace eval(parse()) parameter parsing with parse_numeric_vector() in R/runIchorCNA.R, R/createPanelOfNormals.R, R/plotIchorCNAzoom.R, and scripts/snakemake/code/plotIchorCNAzoom.R - Restore scripts/snakemake/ from v0.4.1 - Add scripts/runIchorCNA.R, a CLI wrapper around run_ichorCNA() so Snakemake and config.yaml work unchanged - Bump DESCRIPTION to 0.7.1
ichorCNA::HMMsegment always resolved to whatever ichorCNA package was installed system-wide, ignoring the version sourced via config.yaml's libdir. Unqualified call matches how the old scripts/runIchorCNA.R invoked it.
The per-solution folder name (solution_optimal_n<N>_p<P>) depends on
the estimated purity/ploidy, so it can't be known before the rule
runs. Snakemake's directory() output only checks the folder exists,
matching the actual .../{tumor}/{tumor}/solution_optimal_n.../ layout.
Corrected the version link for the Nextflow pipeline in the README.
Updated chromosome list format for clarity and compatibility with hg38 and hg19.
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