sort published files so common bioinformatics indexes are processed at the end.

[lindenb]

Hi, this small PR is related to the following issue:

https://github.com/nextflow-io/nextflow/issues/1489

When publishing a set of paths, reorder the files so the common indexes (TBI, BAI,CSI...) are copied at the end, so the timestamps of the files are always older than their indexes (otherwise most tools will fail or emit a warning)

I understand that this is specific to bioinformatics, feel free to reject the PR.

I'm not a groovy programmer so I hope it's the right way and the right place to insert that code. I'm not even sure the files are copied in the order of the List :sweat_smile:

P.

[pditommaso]

I'm find with this but it should be enabled by adding a sort option to the publishDir

[lindenb]

@pditommaso thanks,

I'll try to add the option in the next days.