Nextflow lint results

Generated: 2026-06-16T20:26:44.657755399Z
Nextflow version: 26.04.3
Summary: 12 errors, 31 warnings

❌ Errors

Error: modules/local/hicpro/dnase_mapping_stats.nf:2:10: sample is not defined
```
    tag "$sample = $bam"
         ^^^^^^^
```

Error: subworkflows/local/compartments/main.nf:26:28: cool is already declared

            cool.map{meta, cool, res -> [meta, cool] },
                           ^^^^

Error: subworkflows/local/cooler/main.nf:43:47: pairs is already declared

    cload_inputs = pairs_res.multiMap { meta, pairs, index, cool_bin ->
                                              ^^^^^

Error: subworkflows/local/hicpro/main.nf:18:5: meta was assigned but not declared
```
    meta = row[0].clone()
    ^^^^
```
Error: subworkflows/local/hicpro/main.nf:19:5: meta is not defined
```
    meta.remove('chunk')
    ^^^^
```
Error: subworkflows/local/hicpro/main.nf:20:13: meta is not defined
```
    return [meta, row[1]]
            ^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:140:13: completionEmail is not defined
```
            completionEmail(
            ^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:153:13: imNotification is not defined
```
            imNotification(summary_params, hook_url)
            ^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:292:9: meta was assigned but not declared
```
        meta = row[0].clone()
        ^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:293:9: meta is not defined
```
        meta.chunk = i
        ^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:294:9: meta is not defined
```
        meta.part = row[1].size()
        ^^^^
```
Error: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:295:17: meta is not defined
```
        map += [meta, file]
                ^^^^
```

⚠️ Warnings

Warning: main.nf:73:5: Emit name should be omitted when there is only one emit

    multiqc_report = HIC.out.multiqc_report // channel: /path/to/multiqc_report.html
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: modules/local/hicexplorer/hicPlotDistVsCounts.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/split_cooler_dump/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/compartments/main.nf:26:34: Parameter was not used -- prefix with _ to suppress warning
```
            cool.map{meta, cool, res -> [meta, cool] },
                                 ^^^
```
Warning: subworkflows/local/cooler/main.nf:60:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_cool.map{[it[0], it[1], ""]}
                     ^^
```
Warning: subworkflows/local/cooler/main.nf:60:29: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_cool.map{[it[0], it[1], ""]}
                            ^^
```
Warning: subworkflows/local/cooler/main.nf:72:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it[2] == it[3] }
                 ^^
```
Warning: subworkflows/local/cooler/main.nf:72:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it[2] == it[3] }
                          ^^
```
Warning: subworkflows/local/cooler/main.nf:85:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        COOLER_BALANCE.out.cool.map{[it[0], it[1], ""]}
                                     ^^
```
Warning: subworkflows/local/cooler/main.nf:85:45: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        COOLER_BALANCE.out.cool.map{[it[0], it[1], ""]}
                                            ^^
```
Warning: subworkflows/local/pairtools/main.nf:66:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            single: it[0].part <=1
                    ^^
```
Warning: subworkflows/local/pairtools/main.nf:67:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multiple: it[0].part > 1
                      ^^
```
Warning: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:29:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:32:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:33:5: Parameter was not used -- prefix with _ to suppress warning
```
    help              // boolean: Display help message and exit
    ^^^^
```
Warning: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning
```
    help_full         // boolean: Show the full help message
    ^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_hic_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    show_hidden       // boolean: Show hidden parameters in the help message
    ^^^^^^^^^^^
```
Warning: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5: Emit name should be omitted when there is only one emit
```
    dummy_emit = true
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5: Variable was declared but not used
```
    valid_config = checkConfigProvided()
    ^^^^^^^^^^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5: Emit name should be omitted when there is only one emit
```
    valid_config
    ^^^^^^^^^^^^
```
Warning: subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5: Emit name should be omitted when there is only one emit
```
    dummy_emit = true
    ^^^^^^^^^^^^^^^
```
Warning: workflows/hic.nf:38:5: Parameter was not used -- prefix with _ to suppress warning
```
    ch_restriction_site
    ^^^^^^^^^^^^^^^^^^^
```

Warning: workflows/hic.nf:97:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def paired = files.findAll { it.name =~ /_val_[12]\.fq\.gz$/ }
                                         ^^

Warning: workflows/hic.nf:110:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
                                                                   ^^

Warning: workflows/hic.nf:155:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                     ^^
```
Warning: workflows/hic.nf:155:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                                         ^^
```
Warning: workflows/hic.nf:170:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                     ^^
```
Warning: workflows/hic.nf:170:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                                         ^^
```
Warning: workflows/hic.nf:187:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                     ^^
```
Warning: workflows/hic.nf:187:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[0].resolution == it[2] }
                                         ^^
```

Warning: workflows/hic.nf:254:5: Emit name should be omitted when there is only one emit

    multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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