Nextflow lint results

Generated: 2026-01-16T10:27:07.757239844Z
Nextflow version: 25.12.0-edge
Summary: 33 errors, 22 warnings

❌ Errors

Error: conf/test.config:21:1: Variable declarations cannot be mixed with config statements

def caseRoot = params.pipelines_testdata_base_path + "rarevariantburden/case"
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test.config:32:23: caseRoot is not defined

    caseJointVCF = "${caseRoot}/samples.1KG.chr21-22.vcf.gz"
                      ^^^^^^^^

Error: conf/test.config:33:21: caseRoot is not defined

    caseSample = "${caseRoot}/samples.txt"
                    ^^^^^^^^

Error: conf/test.config:49:35: caseRoot is not defined

    caseAnnotatedVCFFileList = "${caseRoot}/annotationFiles.csv"
                                  ^^^^^^^^

Error: conf/test.config:51:36: caseRoot is not defined

    caseAnnotationGDSFileList = "${caseRoot}/annotationGDSFiles.csv"
                                   ^^^^^^^^

Error: conf/test.config:53:34: caseRoot is not defined

    caseGenotypeGDSFileList = "${caseRoot}/genotypeGDSFiles.csv"
                                 ^^^^^^^^

Error: conf/test.config:55:25: caseRoot is not defined

    casePopulation = "${caseRoot}/casePopulation.txt"
                        ^^^^^^^^

Error: main.nf:104:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
workflow.onComplete {
^
```

Error: modules/local/cocorv/main.nf:6:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:33:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:56:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:81:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:103:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:136:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:206:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:228:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:253:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:278:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:301:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:322:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:352:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:374:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:480:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:522:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:552:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:585:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/cocorv/main.nf:612:5: Invalid process directive

    ext.singularity_pull_docker_container = true
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: nextflow.config:337:41: manifest is not defined

\033[0;35m  nf-core/rarevariantburden ${manifest.version}\033[0m
                                        ^^^^^^^^

Error: nextflow.config:340:26: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                         ^^^^^^^^

Error: nextflow.config:340:69: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                    ^^^^^^^^

Error: nextflow.config:340:186: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                                                                         ^^^^^^^^

Error: nextflow.config:349:22: validation is not defined

        beforeText = validation.help.beforeText
                     ^^^^^^^^^^

Error: nextflow.config:350:21: validation is not defined

        afterText = validation.help.afterText
                    ^^^^^^^^^^

⚠️ Warnings

Warning: main.nf:159:25: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        it.name.matches(pattern.replace('*', '.*'))
                        ^^

Warning: main.nf:161:25: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        it.copyTo("${destDir}/${it.name}")
                        ^^

Warning: main.nf:161:49: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        it.copyTo("${destDir}/${it.name}")
                                                ^^

Warning: main.nf:162:46: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        log.info "✓ Copied ${it.name} to ${destDir}"
                                             ^^

Warning: nextflow.config:340:129: Implicit closure parameter is deprecated, declare an explicit parameter instead

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                ^^

Warning: subworkflows/local/utils_nfcore_rarevariantburden_pipeline/main.nf:31:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```

Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:98: The use of Channel to access channel factories is deprecated -- use channel instead

    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
                                                                                                 ^^^^^^^

Warning: workflows/rarevariantburden.nf:39:5: Parameter was not used -- prefix with _ to suppress warning
```
    caseJointVCF // caseJointVCF read in from --caseJointVCF
    ^^^^^^^^^^^^
```
Warning: workflows/rarevariantburden.nf:40:5: Parameter was not used -- prefix with _ to suppress warning
```
    caseSample // caseSample read in from --caseSample
    ^^^^^^^^^^
```
Warning: workflows/rarevariantburden.nf:46:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        intersectChannel = Channel.value(params.controlBed)
                           ^^^^^^^
```
Warning: workflows/rarevariantburden.nf:54:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    chromChannel = Channel.fromList(Arrays.asList(chromosomes))
                   ^^^^^^^
```
Warning: workflows/rarevariantburden.nf:65:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        caseVCF_ch = Channel
                     ^^^^^^^
```

Warning: workflows/rarevariantburden.nf:76:34: The use of Channel to access channel factories is deprecated -- use channel instead

            normalizeQCChannel = Channel
                                 ^^^^^^^

Warning: workflows/rarevariantburden.nf:103:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        annotateChannel = Channel
                          ^^^^^^^
```
Warning: workflows/rarevariantburden.nf:120:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
        caseGenotypeGDSChannel = Channel
                                 ^^^^^^^
```

Warning: workflows/rarevariantburden.nf:126:36: The use of Channel to access channel factories is deprecated -- use channel instead

        caseAnnotationGDSChannel = Channel
                                   ^^^^^^^

Warning: workflows/rarevariantburden.nf:152:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
        populationChannel = Channel.value(params.casePopulation)
                            ^^^^^^^
```
Warning: workflows/rarevariantburden.nf:158:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    controlGenotypeGDSChannel = Channel
                                ^^^^^^^
```
Warning: workflows/rarevariantburden.nf:163:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
    controlAnnotationGDSChannel = Channel
                                  ^^^^^^^
```

Warning: workflows/rarevariantburden.nf:191:45: Implicit closure parameter is deprecated, declare an explicit parameter instead

    mergeCoCoRVResults(cocorvOutChannel.map{it[1]}.collect(), cocorvOutChannel.map{it[2]}.collect(),
                                            ^^

Warning: workflows/rarevariantburden.nf:191:84: Implicit closure parameter is deprecated, declare an explicit parameter instead

    mergeCoCoRVResults(cocorvOutChannel.map{it[1]}.collect(), cocorvOutChannel.map{it[2]}.collect(),
                                                                                   ^^

Warning: workflows/rarevariantburden.nf:192:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        cocorvOutChannel.map{it[3]}.collect())
                             ^^
```

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