`grch37: false` can only be set once while `grch37: true` can be set per callset

snakemake-workflows / dna-seq-benchmark

A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets

MIT License

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`grch37: false` can only be set once while `grch37: true` can be set per callset #99

Open famosab opened 3 months ago

famosab commented 3 months ago

The flag grch37 is used to define the reference genome used during variant calling in the config.

Expected behavior: Define the reference genome per callset and consequently use the correct rename-contigs contigs file (grch37_ucsc2ensembl or grch38_ucsc2ensembl).

Current behavior: For specific callsets grch37: true can be defined but setting grch37: false per callset does not work. The file for rename contigs has to be set manually.

famosab commented 1 week ago

Other issue with presets.yaml:

high_coverage: true works high_coverage: false does not work, if its not set its set to false