"tw pipelines add/update" unable to specify a path to tower.yml in monorepo

[starnsd]

We have pipelines in a mono repo (main.nf is not at root of repo), and have been using tw pipelines add to deploy pipelines automatically. However, even though the tower.yml file is located next to main.nf, it is not picked up by the command. Unlike the nextflow_schema.json which can be specified via the argument --schema-name, tower.yml does not have an argument to specify the path. It is probably better to have arguments to specify all of the required files (nextflow.config, main.nf, nextflow_schema.json, tower.yml).

Currently we are manually copying the tower.yml file contents in the GUI after pipeline deployment, resulting in the inability to deploy automatically.

[canny]

This issue has been linked to a Canny post: "tw pipelines add/update" unable to specify a path to tower.yml in monorepo 🎉