snakemake / snakemake/snakemake
cannot specify functions as input files if there are rule dependencies
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Description
I cannot use the inputs of a rule as a dependency if any of those inputs are functions.
Reproducer:
Consider the following Snakefile:
rule one:
input:
a="a.txt",
b=lambda wildcards: "b.txt",
rule two:
input:
rules.one.input.a,
When run like snakemake -n, rule two fails with error
TypeError in line 9 of /<path/to>/Snakefile:
expected string or bytes-like object
File "/<path/to>/Snakefile", line 9, in <module>
Note that this happens even though two does not depend on the functional input b. The presence of one function as an input is enough to cause the failure.
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First steps
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- Open a pull request that references the issue number.
Research direction
Start with the reproduced Snakefile and run snakemake -n to confirm the TypeError at rules.one.input.a. Trace how rule input dependencies are resolved when another input is a function. Done means rule two can depend on rules.one.input.a without failing because rule one also has the functional input b.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100