Comments (3)
Hi,
Apologies, I am just seeing this as I did not get a notification earlier.
Your paired-end FASTQ files can be in the same directory you cloned from github or you can simply structure it in a new directory named fastq
To run the pipeline, just type snakemake --config ref={ref_genome}
What {users reference genome}
indicates is the path to where your reference genome is stored, it can be in the data/
directory
For example: snakemake --config ref=./data/kleb.fna --cores 4
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Thank you @idolawoye for your response.
I'll let you know if this works.
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I am closing this issue now that it has been 15 days since your response, Let me know if there is anything I can help with
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