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This repository has been archived by the owner on Oct 25, 2021. It is now read-only.
Can this be done at all (I am working with Saccharomyces right now)?
I edited the config.yml to match my paths
After failing with the default command
snakemake all --config input_fastq=<my-path-to-fastq>/ reference_fasta=<my-path-to-fa> threads=64
complaining that all is not a valid Rule
I am now running a more complete command:
snakemake --snakefile ./Snakefile --configfile ./config.yml --jobs 64 eval
I see that the pipeline is using human data to compare to (HG002_SVs_Tier1_v0.6.vcf.gz)
Which Rule(s) should I run for a non human data in order to get the most out of this pipeline?
Thanks
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