I have snakemake workflow in which the python function executed in the 'run:' context returns the path of the output file. I want to capture that as a variable in the Snakefile
provide it to the 'output:' context.
That way I could have my output:
automatically filled. I wonder if there is any way to do this in snakemake. Please let me know.
Further information on the python function: It processes the file provided in the input:
context and returns a single string which is the path of the output file.
The rule looks like this:
rule task01:
input:
"path/to/input.tsv"
run:
from module import function
p=function(metadata=metadata)
# p is the path where the output file needs to be saved
# For that I would like to access the variable p in the `output:` context below
output:
# can I access the variable p here?
from python function executed in the 'run:' context returns the path of the output file, provide that to 'output:' context
No comments:
Post a Comment