Wrong filename in output due to name conflict

As discussed on Gitter with Michael Crusoe.

I have an issue with some output files having a wrong name, which only occurs on some machines. One of the outputs has a trailing _2 in its filename. I traced it down to filename conflict resolution in toil/cwl/cwltoil.py around line 860. However, I have no clue what triggers this name conflict, and I also don’t understand why this results in my output files being renamed to something unexpected. I’m using Toil 5.6.0 and cwltool 3.1.20211107152837.

Attached is an example of the generated output JSON file. According to MC the problem is in lines 972 & 1969. There’s a false positive for a name conflict. Yes, the files have the same name, but they are in different directories predict.json.gz .

┆Issue is synchronized with this Jira Story ┆friendlyId: TOIL-1170

[gmloose]

I created a PR. I’m not sure how to write a test that properly tests this fix, because I haven’t been able to create a small example.

[mr-c]

Fixed in #4139