FIX: Strict syntax for eager/eva

[maxulysse]

---

name: New Config
about: A new cluster config

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[maxulysse]

@jfy133 @TCLamnidis I tried to update this config to work with the coming new syntax (cf nf-co.re/blog/2026/configs-strict-syntax).
Please have a look, and let us know if it's working for you

[TCLamnidis]

testing this today. sorry for the delay

[TCLamnidis]

Preliminary results (still debugging as I'm not sure where the error is coming from):
Trying to set the custom config base and run this profiles throws an error (same thing happens when setting custom_config_version to eager/eva, which is expected):

$ nextflow run nf-core/eager -r 2.5.3 --custom_config_base 'https://raw.githubusercontent.com/nf-core/configs/refs/heads/eager/eva' -profile test,eva,archgen -w temp --outdir results 
N E X T F L O W  ~  version 22.04.5
WARNING: Could not load nf-core/config/eager profiles: https://raw.githubusercontent.com/nf-core/configs/refs/heads/eager/eva/pipeline/eager.config
No such file: Config file does not exist: https://raw.githubusercontent.com/nf-core/configs/refs/heads/eager/eva/pipeline/conf/test.config

While downloading locally and prviding the config with -c throws a different error:

$ nextflow run nf-core/eager -r 2.5.3 -profile test,eva,archgen -w temp --outdir results -c eva.config 
N E X T F L O W  ~  version 22.04.5
Launching `https://github.com/nf-core/eager` [determined_lumiere] DSL1 - revision: 3f9d64ced5 [2.5.3]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/eager v2.5.3
------------------------------------------------------

Invalid method invocation `doCall` with arguments:  on _run_closure5 type

 -- Check script '/home/thiseas_christos_lamnidis/.nextflow/assets/nf-core/eager/main.nf' at line: 31 or see '.nextflow.log' file for more details

[jfy133]

Could it be because the nextflow version is too old I wonder?

[TCLamnidis]

I tried to mimic the nf-core config setup as much as possible locally.
I downloaded eva.config locally, and set up include.config with:

profiles {
    eva {
        includeConfig "/path/to/eva.config"
    }
}

Then ran nextflow run nf-core/eager -r 2.5.3 -profile eva,archgen,test -w temp --outdir results -c include.config

N E X T F L O W  ~  version 22.04.5
Unable to parse config file: '/[...]/include.config'

  Compile failed for sources FixedSetSources[name='/groovy/script/Script4859A5D001FCE1163A6160201FFBB497']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  /groovy/script/Script4859A5D001FCE1163A6160201FFBB497: 638: unable to resolve class MemoryUnit
   @ line 638, column 31.
                 if (obj.compareTo(params.max_memory as MemoryUnit) == 1)
                                   ^
  
  /groovy/script/Script4859A5D001FCE1163A6160201FFBB497: 639: unable to resolve class MemoryUnit
   @ line 639, column 24.
                     return params.max_memory as MemoryUnit
                            ^
  
  /groovy/script/Script4859A5D001FCE1163A6160201FFBB497: 648: unable to resolve class Duration
   @ line 648, column 31.
                 if (obj.compareTo(params.max_time as Duration) == 1)
                                   ^
  
  /groovy/script/Script4859A5D001FCE1163A6160201FFBB497: 649: unable to resolve class Duration
   @ line 649, column 24.
                     return params.max_time as Duration
                            ^
  
  4 errors

So I don't think this approach works? at least not for NXF 22.04.5?

[TCLamnidis]

Re-adding the nextflow.util before the MemoryUnit and Duration stops the errors about configurations.

params.eager_eva_check_max_func = { obj, type ->
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (_) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (_) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (_) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}

The pipeline still fails at startup with error:

 -- Check script '/home/thiseas_christos_lamnidis/.nextflow/assets/nf-core/eager/main.nf' at line: 31 or see '.nextflow.log' file for more details

line 31 in main is:

    NfcoreSchema.validateParameters(params, json_schema, log)

[maxulysse]

@nvnieuwk any idea, you provided the fix

[nvnieuwk]

Yes, parameter functions don't work, I've discussed this config with @jfy133 and we decided that we should keep one DSL1 version of this config for backwards compatibility for now and migrate this to a proper config once the DSL2 version releases

[maxulysse]

Yes, parameter functions don't work, I've discussed this config with @jfy133 and we decided that we should keep one DSL1 version of this config for backwards compatibility for now and migrate this to a proper config once the DSL2 version releases

ok, so what do we do here?