I am trying to add a function to my Plugin that uses the `params`and

workflow

objects from the current Nextflow run to generate some pre-formatted text however when I write the function, I am doing it like this;

@Function
    String makeTable(Map params, Map workflow, Map manifest, List bad_params){
}

I am not sure if this is the best way to write the function? Should I be passing the

params

and

workflow

objects as input args to the function? It seems like it might not be a great idea to try to get them from implicit environment variables at runtime. However since I am typing these input args as

Map

I am not sure if this is gonna actually break in my Nextflow pipeline when I use it like this

include { makeTable } from 'plugin/nf-myutils'
makeTable(params: params, workflow: workflow, manifest: workflow.manifest, bad_params: ['foo_key'])

it keeps breaking with errors like this

nextflow.exception.MissingProcessException: Missing process or function makeTable([[params:[:], workflow:repository: null, projectDir: /Users/.../examples, commitId: null, revision: null, startTime: 2024-03-21T15:12:05.581281-04:00, endTime: null, duration: null, container: {}, commandLine: nextflow run examples/test.nf, nextflow: nextflow.NextflowMeta(version:23.10.1, build:5891, timestamp:12-01-2024 22:01 UTC, preview:nextflow.NextflowMeta$Preview@35d60381, enable:nextflow.NextflowMeta$Features@68ab6ab0, dsl2:true, dsl2Final:true, strictModeEnabled:false), success: false, workDir: /Users/.../work, launchDir: /Users/.../nf-myutils, profile: standard, manifest:nextflow.config.Manifest@5c4cc644, bad_params:[foo_key]]]) -- Did you mean 'makeTable' instead?

not sure what is wrong with this? Does it not like the typing of the Nextflow

params

and

workflow

objects I am trying to pass?

You're using python syntax Try with

include { makeTable } from 'plugin/nf-myutils' 

makeTable(params, workflow, workflow.manifest, ['foo_key'])

I tried that and it gives the same error

Try to simplify and increase step by step. Fisrt try without args, next with param and so on.

well it works in the test case...

def 'should return a workflow table' () {
        given:
        def example = new ExampleFunctions()
        example.init(new Session([:]))
        def params = ['foo': 1, 'bar': 2, "buzzzz": 5]
        def bad_params = ["buzzzz"]
        def workflow = ['baz': 3]
        def manifest = ['buzz': 4]
        def expected = """
some text goes here
"""
        when:
        def result = example.makeTable(params, workflow, manifest, bad_params)
        println result

        then:
        result == expected
    }

Strange Maybe nextflow version? If you can share the repo maybe I can take a look tomorrow

its here https://github.com/stevekm/nf-niceutils I can build and test fine

./gradlew test

but when I try to run in a real pipeline, its giving these errors shown

./nextflow run examples/test.nf