Nextflow lint results

Generated: 2026-03-14T00:23:19.447674531Z
Nextflow version: 26.02.0-edge
Summary: 10 errors, 28 warnings

❌ Errors

Error: subworkflows/local/concordance_analysis/main.nf:37:22: Unexpected input: 'i'

            for (int i = 0; i < items.size(); i++) {
                     ^

Error: subworkflows/local/prepare_vcfs_test/main.nf:164:25: vcf is already declared

        .branch { meta, vcf, tbi ->
                        ^^^

Error: subworkflows/local/prepare_vcfs_test/main.nf:175:45: vcf is already declared

        ch_branched_vcf.needs_gt.map{ meta, vcf, _tbi -> tuple(meta, vcf) },
                                            ^^^

Error: subworkflows/local/sv_vcf_conversion/main.nf:86:19: input is already declared
```
        .branch { input ->
                  ^^^^^
```

Error: subworkflows/local/sv_vcf_conversion/main.nf:135:19: input is already declared

            .map{ input ->
                  ^^^^^

Error: subworkflows/local/wittyer_benchmark/main.nf:36:41: bed is already declared

            .map{ meta, vcf, truth_vcf, bed -> [meta, vcf, truth_vcf, bed, []] }
                                        ^^^

Error: workflows/variantbenchmarking.nf:32:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/variantbenchmarking/subworkflows/local/concordance_analysis/main.nf'
```
include { CONCORDANCE_ANALYSIS        } from '../subworkflows/local/concordance_analysis'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/variantbenchmarking.nf:249:7: CONCORDANCE_ANALYSIS is not defined
```
      CONCORDANCE_ANALYSIS(
      ^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/variantbenchmarking.nf:256:43: CONCORDANCE_ANALYSIS is not defined

        ch_reports       = ch_reports.mix(CONCORDANCE_ANALYSIS.out.summary_reports)
                                          ^^^^^^^^^^^^^^^^^^^^

Error: workflows/variantbenchmarking.nf:257:41: CONCORDANCE_ANALYSIS is not defined

        evals_ch         = evals_ch.mix(CONCORDANCE_ANALYSIS.out.tagged_variants)
                                        ^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/custom/merge_reports/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/merge_sompy_features/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/custom/plots/main.nf:22:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.benchmark_tool}"
        ^^^^^^

Warning: modules/local/custom/subtract_vcf/main.nf:40:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/happy/happy/main.nf:64:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/ensemble_test_vcfs/main.nf:26:30: Parameter was not used -- prefix with _ to suppress warning
```
    test_vcfs.branch { meta, vcf, index ->
                             ^^^
```

Warning: subworkflows/local/ensemble_test_vcfs/main.nf:26:35: Parameter was not used -- prefix with _ to suppress warning

    test_vcfs.branch { meta, vcf, index ->
                                  ^^^^^

Warning: subworkflows/local/ensemble_test_vcfs/main.nf:37:51: Parameter was not used -- prefix with _ to suppress warning

        branched_vcfs.missing_gt.map { meta, vcf, index -> tuple(meta, vcf) },
                                                  ^^^^^

Warning: subworkflows/local/ensemble_test_vcfs/main.nf:53:49: Parameter was not used -- prefix with _ to suppress warning

        ch_test_vcfs = ch_ready_for_merge.map { meta, vcf, index ->
                                                ^^^^

Warning: subworkflows/local/ensemble_test_vcfs/main.nf:96:37: Parameter was not used -- prefix with _ to suppress warning

        ch_test_vcfs = vcf_ch.map { meta, vcf ->
                                    ^^^^

Warning: subworkflows/local/intersect_statistics/main.nf:20:13: Variable was declared but not used
```
        def meta         = input[0]
            ^^^^
```
Warning: subworkflows/local/prepare_vcfs_test/main.nf:62:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    vcf_ch = Channel.empty()
             ^^^^^^^
```
Warning: subworkflows/local/prepare_vcfs_test/main.nf:164:25: Parameter was not used -- prefix with _ to suppress warning
```
        .branch { meta, vcf, tbi ->
                        ^^^
```
Warning: subworkflows/local/prepare_vcfs_test/main.nf:164:30: Parameter was not used -- prefix with _ to suppress warning
```
        .branch { meta, vcf, tbi ->
                             ^^^
```

Warning: subworkflows/local/sompy_benchmark/main.nf:23:34: Parameter was not used -- prefix with _ to suppress warning

        input_ch.map{meta, test, test_index, truth, truth_index, regions, target -> [meta, test, truth, regions, target]},
                                 ^^^^^^^^^^

Warning: subworkflows/local/sompy_benchmark/main.nf:23:53: Parameter was not used -- prefix with _ to suppress warning

        input_ch.map{meta, test, test_index, truth, truth_index, regions, target -> [meta, test, truth, regions, target]},
                                                    ^^^^^^^^^^^

Warning: subworkflows/local/sv_vcf_conversion/main.nf:43:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        out_vcf_ch = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/sv_vcf_conversion/main.nf:105:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
        out_vcf_ch = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf:32:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_variantbenchmarking_pipeline/main.nf:104:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/local/vcf_variant_filtering/main.nf:28:36: Parameter was not used -- prefix with _ to suppress warning
```
            vcf_ch.map{ meta, vcf, index -> tuple(meta, vcf)}
                                   ^^^^^
```
Warning: workflows/variantbenchmarking.nf:229:13: Variable was declared but not used
```
        def meta = it[0]
            ^^^^
```
Warning: workflows/variantbenchmarking.nf:229:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        def meta = it[0]
                   ^^
```
Warning: workflows/variantbenchmarking.nf:230:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        def regions_file = it[2]
                           ^^
```

Warning: workflows/variantbenchmarking.nf:283:85: Parameter was not used -- prefix with _ to suppress warning

        ch_multiqc_files = ch_multiqc_files.mix(SV_GERMLINE_BENCHMARK.out.logs.map{ meta, log -> log })
                                                                                    ^^^^

Warning: workflows/variantbenchmarking.nf:399:118: Parameter was not used -- prefix with _ to suppress warning

    ch_multiqc_files                      = ch_multiqc_files.mix(REPORT_BENCHMARK_STATISTICS.out.merged_reports.map{ meta, report -> report }.flatten())
                                                                                                                     ^^^^

Warning: workflows/variantbenchmarking.nf:400:82: Parameter was not used -- prefix with _ to suppress warning

    ch_multiqc_files                      = ch_multiqc_files.mix(ch_reports.map{ meta, report -> report }.flatten())
                                                                                 ^^^^

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