Specifying empty params (e.g. clusterOptions in profile) breaks with nf-validation 0.3.1

[pontus]

When running one of the pipelines using nf-validation with 0.3.1 and specifying the UPPMAX profile, it fails with an error:

pontus@lalage:/tmp$ nextflow run nf-core/atacseq -r 2.1.1 -profile uppmax
N E X T F L O W  ~  version 23.04.2
Launching `https://github.com/nf-core/atacseq` [nostalgic_euler] DSL2 - revision: 415795d3c1 [2.1.1]
ERROR ~ JSONObject["project"] not found.

 -- Check script '/home/pontus/.nextflow/assets/nf-core/atacseq/main.nf' at line: 52 or see '.nextflow.log' file for more details
pontus@lalage:/tmp$ 

after some digging, it seems to me this is because the profile sets that up in params, although with a null value.

It looks to me that is enough to have it seen by nf-validation, but when nf-validation tries to report it (

nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

Line 315 in 01a3131

warnings << "* --${specifiedParam}: ${paramsJSON[specifiedParam]}".toString()

) it's not found in paramsJSON because that's based on the cleaned version (

nf-validation/plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

Line 271 in 01a3131

def paramsJSON = new JSONObject(new JsonBuilder(cleanedParams).toString())

) which has removed anything evaluating to false.

A workaround (that makes sense) for now is to ignore the affected param, but this seems to be a bug that can be difficult to figure out and would be nice to have fixed.

[pontus]

And upon rechecking, this is probably the same as #48.

[ewels]

Closing as hopefully solved in #89, which I just merged. Shout if that's not the case, and thanks for reporting @pontus 🙏🏻