Phoenix v2.2.0 error when running in Terra

[neranjan007]

Description of the bug

Hi,
When running v2.2.0 in Terra with inputs:
{
"phoenix_workflow.kraken2db":"${workspace.Kraken2_db_2025}",
"phoenix_workflow.mode":"PHOENIX",
"phoenix_workflow.read1":"${this.read1}",
"phoenix_workflow.read2":"${this.read2}",
"phoenix_workflow.samplename":"${this.phoenix-Key_id}"
}

It seems to give the following error:

Bad output 'phoenix.ncbi_biosample': IllegalArgumentException: No coercion defined from wom value(s) '[]' of type 'Array[Nothing]' to 'File?'.

Thanks

Command used and terminal output

Relevant files

No response

System information

No response

[jvhagey]

Hi @neranjan007 thanks for letting us know about this. I haven't seen this before, but made a small change to address this, can you try running these on the v2.3.0-dev branch and tell me if it is fixed? It ran fine on my side.

[neranjan007]

Hi @jvhagey , thanks for looking into this. I ran the v2.3.0-dev on Terra, and it ran with out any problems. Thanks for the quick fix.

[jvhagey]

yay! We plan to put out a new patch v2.2.1 soon (depending on how long any lapse in funding might be) that will contain this fix as well as a few others. I will leave v2.3.0-dev available on Terra, but since its dev its going to have code changes as we get everything ready for release. So thats the one warning about using dev version. If you want to get into the nitty gritty of what is changing see the changelog.md and the commit history. I will close this once we get the release out so you will get pinged and know its complete.

[neranjan007]

Thanks, I will keep an eye on the new patch.
The above error was initially seen by NJDPH, and when we (CT) tried we also saw it as well.

[jvhagey]

Can you pass this info along to NJDPH as well then so they are aware of the fix? Thanks!

[neranjan007]

Yes, I already did and they did test on their end as well. which seems to work.