Two config files for one Snakemake file

Question

[Xiaokang]

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?

Answer 1

[Bastien Hervé]

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

[Xiaokang]

Thank you! To make the Snakemake file clean, specifying the config file in the command line is a good option!