Allow for failed wildcards in Snakemake workflow
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9 months ago
mrmrwinter ▴ 30

Hi,

I have a snakemake workflow that contains a small section with several shell command rules and external python script rules.

The rules iterate over a wildcard, {OG}, which is created at the beginning of the workflow.

At each rule, some of the wildcards will fail. The successful ones should be passed to the next rule. However, snakemake fails on subsequent rules due to the required input file being missing, as a result of it failing a previous rule.

i have looked into dynamic inputs and checkpoints, but I cant seem to get it to work and the documentation is thin.

My question is, how can I make snakemake reevaluate the wildcard after each rule, so as not to hit errors with missing inputs?

Thanks

snakemake python wildcards • 290 views
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Hi I am running into exactly the same problem. Did you ever encounter a solution to this?

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