Fabian Lehmann

I think this problem was related to my PR (https://github.com/nextflow-io/nextflow/pull/2787) and should be fixed in the newest Nextflow version.

Hi @pditommaso, thank you for pointing out the tests. I published my test case. I rewrote my first suggestion, as it had problems if Nextflow had already moved the destination...

Hi @pditommaso, I updated the test case to DSL 2. Furthermore, I forgot to add `-process.scratch true -process.stageOutMode move` in the test case. I also added it now. So the...

Thanks a lot for your review, @pditommaso. This PR is required if you create a symlink in a task but only define the symlink as an output, and you then...

Copying works fine, this only applies to: `-process.scratch true -process.stageOutMode move`. In such cases, only the link is moved. You can run my test case with the current Nextflow Version....

I do two things. First, I fetch the symlink, which is what your method does. https://github.com/nextflow-io/nextflow/blob/c59bce7043db1d1fe11470640a3b99ea7cc363df/modules/nextflow/src/main/resources/nextflow/executor/command-run.txt#L124 In the next steps, I try to keep the kind of the symlink. Four...

Someone might assume to work with a relative or absolute path. But this might only apply to rare cases.

Hi @pditommaso, can you please review this PR.

Hi @pditommaso, I am reaching out regarding this PR that has been open for over a year without any action but is still of great interest. This PR allows you...

Thank you very much for getting back on this. Sure, I extended the case in your example to also work for more than one file. Accordingly, you should be able...