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carpentries-incubator / workflows-nextflow

Workflow management with Nextflow and nf-core
https://carpentries-incubator.github.io/workflows-nextflow/
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Should we add a Handling and recovering from errors episode? #29

Closed mahesh-panchal closed 5 months ago

mahesh-panchal commented 3 years ago

I was wondering whether we should add an episode specific to handling and recovering from errors.

It would include how to use the .command.sh and .command.run in the working directories to debug. Perhaps mention some useful directives, e.g. beforeScript or afterScript.

Or should we have something instead on bad coding practice, e.g. downloading files using wget/curl instead of Nextflow's file inbuilt file staging mechanism?

ggrimes commented 3 years ago

I am porting the nextflow training from https://seqera.io/training and one of the episodes I haven't include is

https://seqera.io/training/#_errors_handling_troubleshooting

This could be added as a lesson.

mahesh-panchal commented 2 years ago

I think it's a good idea to have trouble shooting workflows as a lesson.

https://seqera.io/training/#_error_handling_troubleshooting has a nice start but doesn't really help a lot with the actual troubleshooting.

I've made #64 to turn into a glossary, and we can use it for some challenges.

Or should we have something instead on bad coding practice, e.g. downloading files using wget/curl instead of Nextflow's file inbuilt file staging mechanism?

Added as part of an episode on coding practices.