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isugifNF / polishCLR

A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
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Mitogenome missing error #41

Closed Astahlke closed 1 year ago

Astahlke commented 2 years ago

It would be beneficial to get meaningful errors when the inputs are not provided but are required. For instance, the absence of the mitogenome when using a FALCON-unzipped assemblies causes the workflow to fail with no useful error message.

Astahlke commented 1 year ago

Is this resolved with https://github.com/isugifNF/polishCLR/pull/55? Can the pipeline run now without a mitogenome? Splits included?

j23414 commented 1 year ago

It would be beneficial to get meaningful errors when the inputs are not provided but are required

and

Is this resolved with https://github.com/isugifNF/polishCLR/pull/55?

Yes, it's resolved with #55 such as

https://github.com/isugifNF/polishCLR/blob/b44d194006df1c6a5bc2e08f04c5fda8acaa4743/main.nf#L208-L216

j23414 commented 1 year ago

Can the pipeline run now without a mitogenome? Splits included?

Yes, splits was generalized so mitogenome is not required:

https://github.com/isugifNF/polishCLR/blob/b44d194006df1c6a5bc2e08f04c5fda8acaa4743/modules/helper_functions.nf#L62-L75