Support custom pre-run and config scripts - Githubissues

seqeralabs / showcase-automation

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Support custom pre-run and config scripts #26

Closed adamrtalbot closed 2 months ago

adamrtalbot commented 2 months ago

This PR adds the ability to customise the pre-run script or nextflow.config at runtime. Currently, it does this via a string input so you have to specify --pre_run 'export NXF_VER=23.10.1', this limits its usefulness for large scripts and config files but means it can easily be used with the Github Action runner.

Changes:

Can add pre-run and configs via YAML or via CLI
CLI takes precedence over YAML
Implemented in Github Action
Use string as input and populate a text file - fairly limited in scope

Key questions:

this solves the immediate use case of setting the Nextflow version.
Are we likely to use larger pre-run scripts and configs in this workflow?
Do we want to support files instead.

After this change, Github Action will look like this:

pditommaso commented 2 months ago

I don't see a strong need for files right now