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naobservatory / mgs-workflow

MIT License
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nextflow.config defines script_dir path as script_dir = "${projectDir}/../repo/scripts/" but "repo" should either be mgs-workflow or a variable. #1

Closed simonleandergrimm closed 3 months ago

simonleandergrimm commented 6 months ago

https://github.com/naobservatory/mgs-workflow/blob/5da3ea8710ace7393fa597ad580c13ab3ab9c188/configs/index.config#L29

nextflow.config defines the script_dir path as script_dir = "${projectDir}/../repo/scripts/" but repo should either be a placeholder, mgs-workflow, or a variable that gets defined earlier. E.g.:

repo_dir = "mgs-worfklow"
script_dir = "${projectDir}/../{repo_dir}/scripts/"
willbradshaw commented 3 months ago

The user is responsible for setting their config file to point to the right places; as the developer I don't know what the repo directory will be called (mine is called "repo", yours is called "mgs-workflow") or where it will be relative to the launch directory.

That said, this specific instantiation of this issue will shortly become moot with the new version of the pipeline I'm currently finalizing.