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QuaC - First major review

Merged Manavalan Gajapathy requested to merge make_it_production_ready into master
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@@ -34,11 +34,21 @@ def create_snakemake_command(args):
@@ -34,11 +34,21 @@ def create_snakemake_command(args):
# use absolute path to run it from anywhere
# use absolute path to run it from anywhere
snakefile_path = repo_path / "workflow" / "Snakefile"
snakefile_path = repo_path / "workflow" / "Snakefile"
 
quac_configs = {
 
"modules": args.modules,
 
"project_name": args.project_name,
 
"ped": args.pedigree,
 
"out_dir": str(Path(args.outdir) / args.project_name),
 
"log_dir": args.log_dir,
 
"exome": args.exome,
 
}
 
quac_configs = " ".join([f"{k}='{v}'" for k, v in quac_configs.items()])
 
# snakemake command to run
# snakemake command to run
cmd = [
cmd = [
"snakemake",
"snakemake",
f"--snakefile '{snakefile_path}'",
f"--snakefile '{snakefile_path}'",
f"--config modules='{args.modules}' project_name='{args.project_name}' ped='{args.pedigree}' out_dir='{args.outdir}' log_dir='{args.log_dir}' exome={args.exome}",
f"--config {quac_configs}",
f"--restart-times {args.rerun_failed}",
f"--restart-times {args.rerun_failed}",
"--use-conda",
"--use-conda",
f"--profile '{snakemake_profile_dir}'",
f"--profile '{snakemake_profile_dir}'",
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