I'm in the process of adding the new release of SBDI-GTDB and GTDB and when I try to run the standard test case but with phyloplacement and skipping qiime, I get the below error. I've merged upstream

dev

, so it seems something crept in during the recent PRs.

$ nextflow run . -resume --outdir results -profile docker,test --dada_ref_taxonomy sbdi-gtdb --run_pplace --skip_qiime
[...]

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --run_pplace (true): Value is [string] but should be [boolean]
* --skip_qiime (true): Value is [string] but should be [boolean]

I will circumvent this for the time being, but will try to have a look as soon as I can unless someone knows what might have occurred and can point to what needs fixing/can provide a fix. (I tried the

--run_pplace true

syntax too -- same effect.)

I could imagine it has something to do with the template update or the nextflow version. I can confirm the issue with a fresh pull of dev with

NXF_VER=26.04.1 nextflow run ampliseq -resume --outdir results -profile test,singularity --dada_ref_taxonomy sbdi-gtdb --run_pplace --skip_qiime

, same with

NXF_VER=26.04.0

, using

NXF_VER=25.10.4

works however. So it appears to be the nextflow version.

After I posted I also got the hunch that it might be Nextflow 26. You got to testing that before me. I will also do some testing and then maybe ask at the Nextflow Slack.

I can open a PR to update nf-schema, parameter types can be added at a later stage I guess 😱