Is there any wat to access the input of a snakemake rule in the output
I have a rule that needs to take a that could come from many different locations, do some processing, then put output in a new path which varies depending on the input. Is it possible to do this with key value pairs like this:
def get_vcf_path():
an input function that gets vcf path
my_dict = {'vcf_input_path' : 'vcf_output_path'}
rule my_rule:
input:
vcf_in_path=get_vcf_path
output:
vcf_out_path= lambda wildcards: my_dict [wildcards.input.vcf_path]
shell:
do stuff
I seem to be having issues. I kind of wonder if snakemake cant have output that is that dynamic because it won't be able to tell which rule outputs satisfy rule all.
• 2,049 views
•
link
1 answer
OP here, I don't think you can: https://groups.google.com/g/snakemake/c/VVyw0b6PYig
• 0 views
•
link
Log in to answer this question.