In step 0 (among others), we create symbolic links to input data. It would help to create relative links instead of absolute. This is necessary for bistro integration and better in general (an analysis directory can then be moved around without breaking links). This can be done with realpath, see this example.
very good point!
this has been fixed thoughout the pipeline in commit 0167cdd using code like ln -s $(realpath --relative-to=$(dirname dest) src) dest
Cheers!
Florent
In step 0 (among others), we create symbolic links to input data. It would help to create relative links instead of absolute. This is necessary for bistro integration and better in general (an analysis directory can then be moved around without breaking links). This can be done with
realpath
, see this example.