fix syncing a pipeline from current directory

nf-core / tools

Python package with helper tools for the nf-core community.

https://nf-co.re

MIT License

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fix syncing a pipeline from current directory #3143

Closed mirpedrol closed 2 months ago

mirpedrol commented 2 months ago

When nf-core pipelines sync was run from the pipeline root directory, a new directory was created and all pipeline files deleted. This overrides the output directory to use the same used by the sync command when the template pipeline is created.