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FINNGEN / autoreporting

MIT License
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Misspecified variable phenoname #144

Closed sinarueeger closed 4 years ago

sinarueeger commented 4 years ago

I am using the parallel wdl, and sometimes it is failing (not sure why). The failing is not the problem though, its whats reported.

The stderr file then displays the following: 

Traceback (most recent call last):
  File "<stdin>", line 118, in <module>
NameError: name 'phenoname' is not defined

(see original stderr file here)

https://github.com/FINNGEN/autoreporting/blob/master/wdl/autoreporting.wdl#L173 is the only instance where phenoname is used. phenoname is defined as String phenoname = basename(phenotype_name,".gz"), phenotype_name being the first column of the tsv file, which should be a string. So not sure what the basename gz is doing there.

Couldn't you just drop the phenoname variable all together and replace it with phenotype_name?

Fedja commented 4 years ago

You can use #145 that uses that variable correctly. Seems String phenoname = basename(phenotype_name,".gz") is a remnant when phename was deduced from filename. It does not do anything for the string as it is so does not hurt. I'll leave that for @Lipastomies

Lipastomies commented 4 years ago

This should not be in the wdl files anymore (as of current master b980f79) . Closing.