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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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Nextflow review @bobturneruk ep10, definition of command wrapper #137

Closed ggrimes closed 3 weeks ago

ggrimes commented 2 months ago

I'm not completely clear on what "The command wrapped used to run the job." means. As far as I can tell by searching, the definition of .command.run is not in the Nextflow docs. It might be better described as "The full Nextflow bash script used to run .command.sh."?

ggrimes commented 2 months ago

Would this work?

A Bash script generated by Nextflow to manage the execution environment of the `.command.sh` script. This script acts as a wrapper around .command.sh. It performs several tasks like setting up the task's environment variables, handling the task's pre and post execution (like moving inputs and outputs to correct locations, logging start and end times, handling errors, and ensuring resource limits are respected

I have made a pull request here https://github.com/carpentries-incubator/workflows-nextflow/pull/138