nanopolish wf expecting medaka output

replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data

https://case-group.github.io/

GNU General Public License v3.0

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nanopolish wf expecting medaka output #134

Closed iferres closed 3 years ago

iferres commented 3 years ago

Greetings! Hope you are doing well.

I think I found a bug. We were getting the following error when running the --nanopolish wf: Access to 'artic_medaka.out' is undefined since process doesn't declare any output

Probably the bug is here: https://github.com/replikation/poreCov/blob/ad970dce96da039e1e63ad66db0cdd92b070212f/workflows/artic_nanopore_nCov19.nf#L54

replikation commented 3 years ago

hi good find and thanks for pointing out the faulty code
this happened during the covarplot implementation
the PR #135 should resolve this issue, you can test this and report back if everything is fine on your end: nextflow run replikation/poreCov -b fix134 (...)

thanks again

PS: i added nanopolish to the dry run so this will not happen again

iferres commented 3 years ago

Hi, sorry for the delay. My colleague just told me it worked, so thanks again for your time. Bests! Ignacio