I have two rules on my Snakefile: one generates several sets of files using wildcards, the other one merges everything into a single file. This is how I wrote it:
chr = range(1,23)
rule generate:
input:
og_files = config["tmp"] + '/chr{chr}.bgen',
output:
out = multiext(config["tmp"] + '/plink/chr{{chr}}',
'.bed', '.bim', '.fam')
shell:
"""
plink \
--bgen {input.og_files} \
--make-bed \
--oxford-single-chr \
--out {config[tmp]}/plink/chr{chr}
"""
rule merge:
input:
plink_chr = expand(config["tmp"] + '/plink/chr{chr}.{ext}',
chr = chr,
ext = ['bed', 'bim', 'fam'])
output:
out = multiext(config["tmp"] + '/all',
'.bed', '.bim', '.fam')
shell:
"""
plink \
--pmerge-list-dir {config[tmp]}/plink \
--make-bed \
--out {config[tmp]}/all
"""
Unfortunately, this does not allow me to track the file coming from the first rule to the 2nd rule:
$ snakemake -s myfile.smk -c1 -np
Building DAG of jobs...
MissingInputException in line 17 of myfile.smk:
Missing input files for rule merge:
[list of all the files made by expand()]
What can I use to be able to generate the 22 sets of files with the wildcard chr
in generate
, but be able to track them in the input of merge
? Thank you in advance for your help
In rule
generate
I think you don't want to escape the{chr}
wildcard, otherwise it doesn't get replaced. I.e.:should be: