# Unable to run the n4s imaging workflow. Inputs are apparently of the wrong type

**URL:** <https://community.seqera.io/t/unable-to-run-the-n4s-imaging-workflow-inputs-are-apparently-of-the-wrong-type/2674>\
**Category:** Training\
**Created:** [May 15, 2026, 2:35pm UTC](https://community.seqera.io/t/unable-to-run-the-n4s-imaging-workflow-inputs-are-apparently-of-the-wrong-type/2674 "2026-05-15T14:35:05Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Chris\_Shave](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/chris_shave/32/2446_2.png) [@Chris\_Shave](https://community.seqera.io/u/Chris_Shave)\
**Post date:** [May 15, 2026, 2:35pm UTC](https://community.seqera.io/t/unable-to-run-the-n4s-imaging-workflow-inputs-are-apparently-of-the-wrong-type/2674/1 "2026-05-15T14:35:06Z")

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I am attempting literally the first step of the imaging workflow, described here: [Part 2: Run nf-core/molkart - training.nextflow.io](https://training.nextflow.io/latest/nf4_science/imaging/02_run_molkart/#12-the-molkart-pipeline)

I have cloned the pipeline and edited the nextflow.config to enable docker. I then attempted to run the command I have been provided.

```auto
nextflow run ./molkart \
  --input 'data/samplesheet.csv' \
  --mindagap_tilesize 90 \
  --mindagap_boxsize 7 \
  --mindagap_loopnum 100 \
  --clahe_pyramid_tile 368 \
  --segmentation_method "cellpose,mesmer,stardist" \
  --outdir results

```

The instructions suggest that this should work now, but I receive the following error:

> ERROR ~ Validation of pipeline parameters failed!
> 
> -- Check ‘.nextflow.log’ file for details  
> The following invalid input values have been detected:
> 
> - --mindagap\_loopnum (100): Value is [string] but should be [integer]
> - --clahe\_pyramid\_tile (368): Value is [string] but should be [integer]
> - --mindagap\_tilesize (90): Value is [string] but should be [integer]
> - --mindagap\_boxsize (7): Value is [string] but should be [integer]

I have looked into the module and (sub)workflow dirs and I cannot even find the processes that are using these parameters. I do not know how to force nextflow to interpret them as integers.

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<div class="post-metadata">

**Author:** ![GeraldineVdA](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/geraldinevda/32/178_2.png) [@GeraldineVdA](https://community.seqera.io/u/GeraldineVdA)\
**Post date:** [May 15, 2026, 2:56pm UTC](https://community.seqera.io/t/unable-to-run-the-n4s-imaging-workflow-inputs-are-apparently-of-the-wrong-type/2674/2 "2026-05-15T14:56:09Z")

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Oh that’s a documentation fail, sorry. That tutorial is also using the v1 syntax, like the nf-core tutorial. You need to run `export NXF_SYNTAX_PARSER=v1` to set the training environment correctly.

This is because nf-core pipelines aren’t yet updated to use V2 syntax (typed params and workflow outputs).

See [Nextflow versions - training.nextflow.io](https://training.nextflow.io/latest/info/nxf_versions/) for more context info.

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**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\
**Post date:** [May 22, 2026, 2:56pm UTC](https://community.seqera.io/t/unable-to-run-the-n4s-imaging-workflow-inputs-are-apparently-of-the-wrong-type/2674/3 "2026-05-22T14:56:55Z")

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Closed on May 22, 2026, 2:56pm UTC

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