Description
While running workflows with TES, I noticed several mismatches between the requests sent by Nextflow to the TES server and the expected data format.
Examples of issues
-
Incorrect file type handling
In some cases, data was actually a file, but Nextflow sent it as a directory:
{
"name": null,
"description": null,
"url": "s3://poiesis/ribap/command/workdir/a7/409f72674fb381d844e1e17d085b31/95",
"path": "/work/95",
"path_prefix": null,
"type": "FILE"
}
-
Regex mismatch
The regex used for patterns did not align correctly, causing unexpected behavior.
-
Nullable fields
TES does not define request fields as nullable, but Nextflow includes null values.
→ Expected: optional fields should be omitted instead of sent as null.
Workaround
To get my use case working, I implemented workarounds in [Poiesis](https://github.com/jaeaeich/poiesis). While this helps locally, it would be much better if Nextflow handled these cases directly.
Description
While running workflows with TES, I noticed several mismatches between the requests sent by
Nextflowto theTESserver and the expected data format.Examples of issues
Incorrect file type handling
In some cases, data was actually a file, but Nextflow sent it as a directory:
{ "name": null, "description": null, "url": "s3://poiesis/ribap/command/workdir/a7/409f72674fb381d844e1e17d085b31/95", "path": "/work/95", "path_prefix": null, "type": "FILE" }Regex mismatch
The regex used for patterns did not align correctly, causing unexpected behavior.
Nullable fields
TES does not define request fields as nullable, but Nextflow includes
nullvalues.→ Expected: optional fields should be omitted instead of sent as
null.Workaround
To get my use case working, I implemented workarounds in [Poiesis](https://github.com/jaeaeich/poiesis). While this helps locally, it would be much better if Nextflow handled these cases directly.