bgzip strelka region bed outside container #39
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| vchr=$(echo {params.cpre}{params.schrm} | sed 's/~/\:/g' | sed 's/23\:/X\:/' | sed 's/24\:/Y\:/' | sed 's/25\:/{params.mito_code}\:/' ) | ||
| vchr=${vchr%:} |
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[P0] Escape braces in region bed shell commands
The new region‑bed rules use Bash parameter expansion (vchr=${vchr%:}) without escaping the braces for Snakemake’s .format call. When Snakemake renders the rule, it treats {vchr%:} as a placeholder and raises KeyError: 'vchr%', so neither the germline nor somatic Strelka jobs can run. The line should use doubled braces, e.g. vchr=${{vchr%:}}, and the same fix is needed in the somatic rule around the corresponding lines.
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Testing
snakemake --lint -s workflow/Snakefile(fails: command not found)https://chatgpt.com/codex/tasks/task_e_68bfd3cce8448331824b59104268e5ca