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microbiomedata / metaAssembly

Workflow for metagenome assembly
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json stats file creation for the long read workflow #22

Open aclum opened 2 weeks ago

aclum commented 2 weeks ago

I can't tell if this is being made or not, if it is list what output variable name is being used in jgi_assembly.wdl to specify it.

vlilanl commented 1 week ago

Long Reads has these two stats files. Do you know which one is needed for automation and does it need to be named stats instead of lr_stats?

https://github.com/microbiomedata/metaAssembly/blob/58c8ad7868c74157bcfdd7022421aadb9d34f646/jgi_assembly.wdl#L89-L90

aclum commented 1 week ago

the finish step for long reads is missing the conversion to json that is happening in the short read workflow. https://github.com/microbiomedata/metaAssembly/blob/58c8ad7868c74157bcfdd7022421aadb9d34f646/shortReads_assembly.wdl#L230