Split files in Snakemake - snakemake

Question

I have a simple question, but I just cannot figure it out myself.
I have a list of inputs (a,b,c). For each input, I need to extract some data (1 to 23):
bcftools view -H a.vcf.gz -r 1 > a_chr1.txt
...
bcftools view -H a.vcf.gz -r 23 > a_chr23.txt
I can do it with FOR loop in the Snakemake rule:
IDS=['a','b','c']
chrs=range(1,23)
rule:
input:
expand("{id}.vcf.gz", id=IDS)
output:
expand("{id}_{chr}.txt", chr=chrs, id=IDS)
run:
for i in IDS:
for c in chrs:
shell("bcftools view -H {i}.vcf.gz -r {c} > {i}_chr{c}.txt")
, but FOR loop does not parallelize it. I need a proper Snakemake-way, smth like below, but it does not work.
IDS=['a','b','c']
chrs=range(1,23)
rule:
input:
expand("{id}.vcf.gz", id=IDS)
output:
expand("{id}_{chr}.txt", chr=chrs, id=IDS)
params:
c=expand("{chr}", chr=chrs)
shell:
"bcftools view -H {input} -r {params.c} > {output}"
Could you please help?

Answer 1

You are not taking advantage of the snakemake wildcards here. If you specify an expand in your inputs and outputs then snakemake will run the rule only once. It tells snakemake that all vcf files are needed to run the rule and that this rule will produce all splitted files. What you need is a rule that can be applied to any vcf file and will produce only one splitted (by chr) output.
IDS=['a','b','c']
chrs=range(1,23)
rule all:
input: expand("{id}_{chr}.txt", chr=chrs, id=IDS)
rule splitByChr:
input:
"{id}.vcf.gz"
output:
"{id}_{chr}.txt"
shell:
"bcftools view -H {input} -r {wildcards.chr} > {output}"
The rule all here will trigger the rule splitByChr as many times as necessary.
Also note that {id} and {chr} in the expand function are not wildcards. They are placeholders for the expand arguments defined.