I am trying to create a pipeline where a small chain of rules are ran on a dynamic number of files output by an earlier rule using output. However, I am getting the following error: "wildcards in input files cannot be determined from output files:".
This suggests to me that what I am trying to do is not currently supported. Here is a pseudo example of what I am trying to do:
rule a:
input: "my static file.txt"
output: dynamic('my/path/{id}.txt')
rule b:
input: dynamic('my/path/{id}.txt')
output: dynamic('my/path/{id}.reprocessed.txt')
rule c:
input: dynamic('my/path/{id}.reprocessed.txt')
output: 'gather.txt'
Running snakemake with
rule all:
input: dynamic('my/path/{id}.txt')
Works without any issues, but when I run snakemake with:
rule all:
input: dynamic('my/path/{id}.reprocessed.txt')
I get the error: "wildcards in input files cannot be determined from output files:"
Is this feature supported? Has anyone successfully made such a chain? Any considerations I need to take into account?
Thanks!
