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Relative directory for pipeline interfaces. #406

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nsheff opened this issue Aug 16, 2023 · 2 comments · Fixed by #408
Closed

Relative directory for pipeline interfaces. #406

nsheff opened this issue Aug 16, 2023 · 2 comments · Fixed by #408
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@nsheff
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nsheff commented Aug 16, 2023

In earlier versions of the looper, the pipeline interface was defined in the PEP (as sample attributes). Relative paths were considered relative to the PEP sample table, I guess.

But 2 things have changed:

  1. In the dev version of looper that introduces looper config, the pipeline interface is defined in the looper config file.
  2. now that looper can get PEPs from PEPhub, what should a relative path be relative to ? In the current implementation, this has been made relative to the current working directory.

This is a problem, because it means I can't just change from a local to a PEPhub PEP, leaving the rest of the file the same. I would also have to change the pipeline interface relative paths.

Shouldn't the pipeline interfaces (and other looper settings) be made relative to the looper config file, now that that's where they're specified (instead of the PEP or sample table)?

@nsheff
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nsheff commented Aug 16, 2023

Related to #344

@donaldcampbelljr
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Closed via #400

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