snakecharm

snakecharm copied to clipboard

Inspection: Cache and bechmark are not reported as an error

3

Snakemake does not allow setting benchmark and cache for the same rule - it should be reported as error, but snakecharm does not detect it https://github.com/snakemake/snakemake/pull/2335 

Xewar313

Version 7.25.0 introduced localrule directive, which is not recognized by Snakecharm https://github.com/snakemake/snakemake/pull/2180

Xewar313

Version 7.13.0 added gitfile option to support using local git repositories https://github.com/snakemake/snakemake/pull/1376, and it is not recognized by snakecharm

Xewar313

When trying to import code from github (and probably gitlab), snakecharm throws error that there is "unresolved reference 'github'", and does not detect imported rule. 

Xewar313

After using import, fuctions from other smk files are not detected

2

Snakecharm does not detect test declaration when it is imported from other file  

Xewar313

``` rule test1: output: "somefile.txt" use rule test1 as test2 with: input: "x.txt" def test(): print(rules.test2.input) print(rules.test2.output) return "result.txt" ```  Second output should resolve to output section in test1...

Xewar313

Should be merged after https://github.com/JetBrains-Research/snakecharm/pull/529 Solves https://github.com/JetBrains-Research/snakecharm/issues/527

Xewar313

https://github.com/JetBrains-Research/snakecharm/issues/500

Xewar313

https://github.com/JetBrains-Research/snakecharm/issues/508

Xewar313

Wildcard not properly defined false warning when typing first input, then output section. Warning disappears if later edit input section.

iromeo