Nextflow lint results

Generated: 2026-03-17T00:23:22.453582215Z
Nextflow version: 26.02.0-edge
Summary: 12 errors, 47 warnings

❌ Errors

Error: main.nf:18:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/differentialabundance/workflows/differentialabundance.nf'
```
include { DIFFERENTIALABUNDANCE   } from './workflows/differentialabundance'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: main.nf:19:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/differentialabundance/subworkflows/local/utils_nfcore_differentialabundance_pipeline/main.nf'

include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_differentialabundance_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:20:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/differentialabundance/subworkflows/local/utils_nfcore_differentialabundance_pipeline/main.nf'

include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_differentialabundance_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:21:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/differentialabundance/subworkflows/local/utils_nfcore_differentialabundance_pipeline/main.nf'

include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_differentialabundance_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:29:14: getGenomeAttribute is not defined

params.gtf = getGenomeAttribute('gtf')
             ^^^^^^^^^^^^^^^^^^

Error: main.nf:50:5: DIFFERENTIALABUNDANCE is not defined

    DIFFERENTIALABUNDANCE (
    ^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:67:5: PIPELINE_INITIALISATION is not defined

    PIPELINE_INITIALISATION (
    ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:84:9: PIPELINE_INITIALISATION is not defined

        PIPELINE_INITIALISATION.out.paramsets
        ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:90:5: PIPELINE_COMPLETION is not defined

    PIPELINE_COMPLETION (
    ^^^^^^^^^^^^^^^^^^^

Error: modules/nf-core/quartonotebook/main.nf:45:5: yamlBuilder is not defined
```
    yamlBuilder(notebook_parameters)
    ^^^^^^^^^^^
```

Error: subworkflows/local/utils_nfcore_differentialabundance_pipeline/main.nf:441:43: Unexpected input: '('

    yaml_content = yaml_content.replaceAll(/\$projectDir/, projectDir.toString())
                                          ^

Error: workflows/differentialabundance.nf:213:96: Unexpected input: '='

    ch_proteus_raw = prepareModuleOutput(PROTEUS.out.raw_tab, ch_paramsets, meta_keys_to_remove=['contrast'])
                                                                                               ^

⚠️ Warnings

Warning: modules/nf-core/custom/filterdifferentialtable/main.nf:25:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/shinyngs/staticexploratory/main.nf:51:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:34:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:93:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

        norm_inputs.contrasts_for_norm_with_formula.filter{it[0].differential_method == 'limma'},
                                                           ^^

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:94:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        norm_inputs.samples_and_matrix.filter{it[0].differential_method == 'limma'}
                                              ^^
```

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:100:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

        inputs.contrasts_for_diff_with_formula.filter{ it[0].differential_method == 'limma' },
                                                       ^^

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:101:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        inputs.samples_and_matrix.filter{ it[0].differential_method == 'limma' }
                                          ^^
```

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:118:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

        norm_inputs.contrasts_for_norm_with_formula.filter{it[0].differential_method == 'deseq2'},
                                                           ^^

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:119:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        norm_inputs.samples_and_matrix.filter{it[0].differential_method == 'deseq2'},
                                              ^^
```
Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:120:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        norm_inputs.control_features.filter{it[0].differential_method == 'deseq2'},
                                            ^^
```
Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:121:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        norm_inputs.transcript_length.filter{it[0].differential_method == 'deseq2'}
                                             ^^
```

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:127:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

        inputs.contrasts_for_diff_with_formula.filter{it[0].differential_method == 'deseq2'},
                                                      ^^

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:128:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        inputs.samples_and_matrix.filter{it[0].differential_method == 'deseq2'},
                                         ^^
```
Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:129:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        inputs.control_features.filter{it[0].differential_method == 'deseq2'},
                                       ^^
```
Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:130:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        inputs.transcript_length.filter{it[0].differential_method == 'deseq2'}
                                        ^^
```
Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:143:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        inputs.contrasts_for_diff.filter{it[0].differential_method == 'propd'},
                                         ^^
```
Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:144:44: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        inputs.samples_and_matrix.filter { it[0].differential_method == 'propd' }
                                           ^^
```

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:166:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

        norm_inputs.contrasts_for_norm_with_formula.filter{it[0].differential_method == 'dream'},
                                                           ^^

Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:167:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        norm_inputs.samples_and_matrix.filter{it[0].differential_method == 'dream'}
                                              ^^
```
Warning: subworkflows/nf-core/abundance_differential_filter/main.nf:172:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        inputs.samples_and_matrix.filter{ it[0].differential_method == 'dream' }
                                          ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:36:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:58:62: Parameter was not used -- prefix with _ to suppress warning

    def criteria = multiMapCriteria { meta, input, genesets, background, method, samplesheet, featuresheet, features_id, features_symbol, meta_contrast, variable, reference, target, formula, comparison ->
                                                             ^^^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:58:154: Parameter was not used -- prefix with _ to suppress warning

    def criteria = multiMapCriteria { meta, input, genesets, background, method, samplesheet, featuresheet, features_id, features_symbol, meta_contrast, variable, reference, target, formula, comparison ->
                                                                                                                                                         ^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:58:164: Parameter was not used -- prefix with _ to suppress warning

    def criteria = multiMapCriteria { meta, input, genesets, background, method, samplesheet, featuresheet, features_id, features_symbol, meta_contrast, variable, reference, target, formula, comparison ->
                                                                                                                                                                   ^^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:58:175: Parameter was not used -- prefix with _ to suppress warning

    def criteria = multiMapCriteria { meta, input, genesets, background, method, samplesheet, featuresheet, features_id, features_symbol, meta_contrast, variable, reference, target, formula, comparison ->
                                                                                                                                                                              ^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:58:183: Parameter was not used -- prefix with _ to suppress warning

    def criteria = multiMapCriteria { meta, input, genesets, background, method, samplesheet, featuresheet, features_id, features_symbol, meta_contrast, variable, reference, target, formula, comparison ->
                                                                                                                                                                                      ^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:58:192: Parameter was not used -- prefix with _ to suppress warning

    def criteria = multiMapCriteria { meta, input, genesets, background, method, samplesheet, featuresheet, features_id, features_symbol, meta_contrast, variable, reference, target, formula, comparison ->
                                                                                                                                                                                               ^^^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:75:19: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, contrastMap, variable, reference, target, formula, comparison ->
                  ^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:75:25: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, contrastMap, variable, reference, target, formula, comparison ->
                        ^^^^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:75:48: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, contrastMap, variable, reference, target, formula, comparison ->
                                               ^^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:75:59: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, contrastMap, variable, reference, target, formula, comparison ->
                                                          ^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:75:67: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, contrastMap, variable, reference, target, formula, comparison ->
                                                                  ^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:75:76: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, contrastMap, variable, reference, target, formula, comparison ->
                                                                           ^^^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:80:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it[4] == 'gsea' }
                 ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:91:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_other.input.filter{ it[0].functional_method == 'gprofiler2' },
                                         ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:92:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_other.genesets.filter{ it[0].functional_method == 'gprofiler2'},
                                            ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:93:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_other.background.filter{ it[0].functional_method == 'gprofiler2'}
                                              ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:119:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_gsea.map{ tuple(it[0].reference, it[0].target) },
                                     ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:119:55: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_gsea.map{ tuple(it[0].reference, it[0].target) },
                                                      ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:127:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_other.input.filter{ it[0].functional_method == 'decoupler' },
                                         ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:128:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_other.genesets.filter{ it[0].functional_method == 'decoupler'},
                                            ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:129:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_other.features.filter{ it[0].functional_method == 'decoupler'}
                                            ^^
```

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:130:41: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, features_sheet, features_id, features_symbol -> [meta, features_sheet] }
                                        ^^^^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:130:54: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, features_sheet, features_id, features_symbol -> [meta, features_sheet] }
                                                     ^^^^^^^^^^^^^^^

Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:138:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_other.input.filter{ it[0].functional_method == 'grea' },
                                         ^^
```
Warning: subworkflows/nf-core/differential_functional_enrichment/main.nf:139:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_input_for_other.genesets.filter{ it[0].functional_method == 'grea' }
                                            ^^
```

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