In my case, there is no pattern in the names of input and output files, so I used a dict to map the output to the input file, and then used this dict in the function as input. Please see the codes of Snakemake file below:
in_files = ['in_a', 'in_b']
out_files = ['out_c', 'out_d']
out_to_in_dict = dict()
for in_file, out_file in zip(in_files, out_files):
out_to_in_dict[out_file] = in_file
rule all:
input:
out_files
rule copy_file:
input:
lambda wildcards: out_to_in_dict[wildcards.outfile]
output:
'{outfile}'
shell:
'''
cp {input} {output}
'''
After executing Snakemake, I got this error:
InputFunctionException in line 8 of /home/test.snake:
KeyError: 'in_a'
Wildcards:
outfile=in_a
The version of Snakemake I am using is 5.5.3. Could anyone please help? Thanks!
I'm not 100% sure why but you can fix it by constraining the scope of the wildcards using wildcard_constraints:
in_files = ['in_a', 'in_b']
out_files = ['out_c', 'out_d']
out_to_in_dict = dict()
for in_file, out_file in zip(in_files, out_files):
out_to_in_dict[out_file] = in_file
wildcard_constraints:
outfile= '|'.join([re.escape(x) for x in out_files]),
rule all:
input:
out_files
rule copy_file:
input:
lambda wildcards: out_to_in_dict[wildcards.outfile]
output:
'{outfile}'
shell:
'''
cp {input} {output}
'''
It's probably related to this https://groups.google.com/forum/#!msg/snakemake/wVlJW9X-9EU/gSZh4U0_CQAJ but just now I don't see why it applies to your example. Personally, I use wildcard_constraints quite liberally as I don't like snakemake's default behaviour of interpreting strings as regexes.