Hello,
I am trying to update a pipeline i created in snakemake version 7.24 and I am running into an issue with providing empty strings as input. This is becoming an issue due to the following:
In a subsequent rule, I say that the input to that rule is either the output of previous rules (which start processing user input files which can be empty) or directly provided by the user like so:
input:
lambda wildcards: "RESULTS/PREPROCESSING/CCS_PACBIO/MERGED/" + PREFIX + "_merged_ccs.fastq" if DO_CCS else config["hifi"]
You can see that I have added a conditional term (DO_CCS) for when we have this file type and want to process it. If that's set to False the input file doesnt exist (set to '') and it defaults to the input from the config.
How can I code this now in the new (9+) version?
Hello,
I am trying to update a pipeline i created in snakemake version 7.24 and I am running into an issue with providing empty strings as input. This is becoming an issue due to the following:
In a subsequent rule, I say that the input to that rule is either the output of previous rules (which start processing user input files which can be empty) or directly provided by the user like so:
You can see that I have added a conditional term (DO_CCS) for when we have this file type and want to process it. If that's set to False the input file doesnt exist (set to '') and it defaults to the input from the config.
How can I code this now in the new (9+) version?