I have one yaml file called config_T11H.yaml with the following content:
# the configuration for workflow of T11H
BASE_EDITOR: T11H
INDIR: data/alignment
OUTDIR: output/output_T11H
# start and end positions of editing window
START: 3
END: 9
and I have another yaml file named config_T11L.yaml with the following content:
# the configuration for workflow of T11L
BASE_EDITOR: T11L
INDIR: data/alignment
OUTDIR: output/output_T11L
# start and end positions of editing window
START: 3
END: 15
I have written a snakemake file base_editing.smk that will run a pipeline with the two sets of parameters in the two yaml files above.
Currently what I am doing is to manually modify the variable configfile in the snakemake file:
Firstly I write configfile: "config_T11H.yaml" at the beginning of the snakemake file, and run the snakemake file snakemake -c 1 -s base_editing.smk;
After it finishes, I then modify the snakemake file configfile: "config_T11L.yaml" and run the snakemake file again snakemake -c 1 -s base_editing.smk.
Is there an easier way to run the snakemake file on the two yaml files with only one-go?
That is exactly what Snakemake is for.
You could create a sample variable at the top of a config.yaml file and loop over these samples in your main snakemake.
samples:
T11H
T11I
T11L
Then, either create a list in your config file associating your samples and their start/end values, or txt file like T11H.txt that your rules would interpret.
You can also call your config_T11H.yaml directly in the command like :
snakemake -c 1 -s base_editing.smk --configfile config_T11H.yaml
Thank you! To make the Snakemake file clean, specifying the config file in the command line is a good option!
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