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dbespiatykh avatar dbespiatykh commented on June 23, 2024

You should configure workflow as described here: https://github.com/dbespiatykh/RDscan/tree/master/config.
In short, you need to add your samples to RDscan/config/samples.tsv like so:

Run_accession R1 R2
your_sample_A /path/to/your_sample_A_1.fastq.gz /path/to/your_sample_A_2.fastq.gz
your_sample_B /path/to/your_sample_B_2.fastq.gz /path/to/your_sample_B_2.fastq.gz

Then you need to run the command you mentioned (inside RDscan directory).
Alternatively, you can use this command (to omit mamba): snakemake --cores all --use-conda.

from rdscan.

stuber avatar stuber commented on June 23, 2024

from rdscan.

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