Currently, your workflow indeed consists in applying the "vep" rule only once, where it executes vep
with all your inputs and outputs as arguments. I don't know how vep
works, but it is likely either failing or not doing what you expect.
You should probably write your rule's input and output without expansion, and drive it using an "all" rule, that does the expand:
CHROMS = [str(c) for c in range(1, 23)] + ["X"]
rule all:
input:
expand("data/vep/split/chr{chrom}.ann.vcf",
chrom=CHROMS)
rule vep:
input:
"data/split/chr{chrom}.vcf"
output:
"data/vep/split/chr{chrom}.ann.vcf"
shell:
"vep "
"{input} "
"{output}"
To generate the desired input of the "all" rule, snakemake will determine how many times and how (i.e. with what value for the chrom
wildcard) it needs to apply the "vep" rule.
Be sure to put the "all" rule before all other rules.
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