[Python] Two config files (same variables but different values) for one Snakemake file

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.

A toy snakemake file is as followed:

configfile: "config/config_T11H.yaml"
# configfile: "config/config_T11L.yaml"

base_editor = config["BASE_EDITOR"]
input_dir = config["INDIR"]
output_dir = config["OUTDIR"]

# editing window
start = config["START"]
end = config["END"]

rule all:
input:
head = output_dir + "/temp_head.txt"

rule files:
input:
files = input_dir
output:
txt = output_dir + "/temp.txt"
params:
editor = base_editor
shell:
"""
ls {input.files} | grep {params.editor} > {output.txt}
"""

rule head:
input:
txt = output_dir + "/temp.txt"
output:
head = output_dir + "/temp_head.txt"
params:
end = int(end)
shell:
"""
head -{params.end} {input.txt} > {output.head}
"""


Is there an easier way to run the snakemake file on the two yaml files with only one-go?

One failed try:

# configfile: "config/config_T11H.yaml"
# configfile: "config/config_T11L.yaml"

configfiles = ["config/config_T11H.yaml", "config/config_T11L.yaml"]

for fn_config in configfiles:
configfile: fn_config
base_editor = config["BASE_EDITOR"]
input_dir = config["INDIR"]
output_dir = config["OUTDIR"]

# editing window
start = config["START"]
end = config["END"]

print(end)

rule all:
input:
head = output_dir + "/temp_head.txt"

rule files:
input:
files = input_dir
output:
txt = output_dir + "/temp.txt"
params:
editor = base_editor
shell:
"""
ls {input.files} | grep {params.editor} > {output.txt}
"""

rule head:
input:
txt = output_dir + "/temp.txt"
output:
head = output_dir + "/temp_head.txt"
params:
end = int(end)
shell:
"""
head -{params.end} {input.txt} > {output.head}
"""


With the error message:

CreateRuleException in file workflow/base_editing.smk, line 19:
The name all is already used by another rule
File "workflow/base_editing.smk", line 19, in <module>

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