Nextflow lint results

Generated: 2026-01-31T00:20:23.153189759Z
Nextflow version: 25.12.0-edge
Summary: 69 errors, 80 warnings

❌ Errors

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

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

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

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

Error: main.nf:60:5: Workflow emit multiqc_report is already declared

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

Error: main.nf:76:5: PIPELINE_INITIALISATION is not defined

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

Error: main.nf:96:36: PIPELINE_INITIALISATION is not defined

    NFCORE_DISEASEMODULEDISCOVERY (PIPELINE_INITIALISATION.out.seeds, PIPELINE_INITIALISATION.out.network, PIPELINE_INITIALISATION.out.shortest_paths, PIPELINE_INITIALISATION.out.perturbed_networks)
                                   ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:96:71: PIPELINE_INITIALISATION is not defined

    NFCORE_DISEASEMODULEDISCOVERY (PIPELINE_INITIALISATION.out.seeds, PIPELINE_INITIALISATION.out.network, PIPELINE_INITIALISATION.out.shortest_paths, PIPELINE_INITIALISATION.out.perturbed_networks)
                                                                      ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:96:108: PIPELINE_INITIALISATION is not defined

    NFCORE_DISEASEMODULEDISCOVERY (PIPELINE_INITIALISATION.out.seeds, PIPELINE_INITIALISATION.out.network, PIPELINE_INITIALISATION.out.shortest_paths, PIPELINE_INITIALISATION.out.perturbed_networks)
                                                                                                           ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:96:152: PIPELINE_INITIALISATION is not defined

    NFCORE_DISEASEMODULEDISCOVERY (PIPELINE_INITIALISATION.out.seeds, PIPELINE_INITIALISATION.out.network, PIPELINE_INITIALISATION.out.shortest_paths, PIPELINE_INITIALISATION.out.perturbed_networks)
                                                                                                                                                       ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:101:5: PIPELINE_COMPLETION is not defined

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

Error: modules/local/graphtoolparser/main.nf:6:36: Unexpected input: ','

    tuple val(meta), (path(network), stageAs: 'input/*')
                                   ^

Error: modules/local/inputcheck/main.nf:6:35: Unexpected input: ','

    tuple val(meta ), (path(seeds), stageAs: 'check/*'), (path(network), stageAs: 'check/*')
                                  ^

Error: modules/local/networkannotation/main.nf:6:39: Unexpected input: ','

    tuple val(meta), (path(subnetwork), stageAs: 'input/*'), (path (network), stageAs: 'input/*')
                                      ^

Error: subworkflows/local/gt_diamond/main.nf:5:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/modules/local/graphtoolparser/main.nf'
```
include { GRAPHTOOLPARSER   } from '../../../modules/local/graphtoolparser/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/gt_diamond/main.nf:20:5: GRAPHTOOLPARSER is not defined

    GRAPHTOOLPARSER(ch_network, "diamond")                                  // Convert gt file to diamond specific format
    ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_diamond/main.nf:21:35: GRAPHTOOLPARSER is not defined

    ch_versions = ch_versions.mix(GRAPHTOOLPARSER.out.versions)             // Collect versions
                                  ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_diamond/main.nf:26:18: GRAPHTOOLPARSER is not defined

        .combine(GRAPHTOOLPARSER.out.network.map{ meta, network -> [meta.network_id, meta, network]}, by: 0)
                 ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_domino/main.nf:6:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/modules/local/graphtoolparser/main.nf'
```
include { GRAPHTOOLPARSER   } from '../../../modules/local/graphtoolparser/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/gt_domino/main.nf:22:5: GRAPHTOOLPARSER is not defined

    GRAPHTOOLPARSER(ch_network, "domino")                                   // Convert gt file to domino specific format, including prefixes
    ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_domino/main.nf:23:35: GRAPHTOOLPARSER is not defined

    ch_versions = ch_versions.mix(GRAPHTOOLPARSER.out.versions)             // Collect versions
                                  ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_domino/main.nf:25:19: GRAPHTOOLPARSER is not defined

    DOMINO_SLICER(GRAPHTOOLPARSER.out.network)                              // Run the DOMINO preprocessing step on the parsed networks
                  ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_domino/main.nf:28:25: GRAPHTOOLPARSER is not defined

    ch_domino_network = GRAPHTOOLPARSER.out.network
                        ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_networkperturbation/main.nf:108:18: Unexpected input: '->'
```
            item -> "  " + item.text,
                 ^
```
Error: subworkflows/local/gt_robust/main.nf:5:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/modules/local/graphtoolparser/main.nf'
```
include { GRAPHTOOLPARSER   } from '../../../modules/local/graphtoolparser/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/gt_robust/main.nf:18:5: GRAPHTOOLPARSER is not defined
```
    GRAPHTOOLPARSER(ch_network, "robust")
    ^^^^^^^^^^^^^^^
```

Error: subworkflows/local/gt_robust/main.nf:19:35: GRAPHTOOLPARSER is not defined

    ch_versions = ch_versions.mix(GRAPHTOOLPARSER.out.versions)
                                  ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_robust/main.nf:24:18: GRAPHTOOLPARSER is not defined

        .combine(GRAPHTOOLPARSER.out.network.map{ meta, network -> [meta.network_id, meta, network]}, by: 0)
                 ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_robust_bias_aware/main.nf:5:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/modules/local/graphtoolparser/main.nf'
```
include { GRAPHTOOLPARSER   } from '../../../modules/local/graphtoolparser/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/gt_robust_bias_aware/main.nf:18:5: GRAPHTOOLPARSER is not defined
```
    GRAPHTOOLPARSER(ch_network, "robust")
    ^^^^^^^^^^^^^^^
```

Error: subworkflows/local/gt_robust_bias_aware/main.nf:19:35: GRAPHTOOLPARSER is not defined

    ch_versions = ch_versions.mix(GRAPHTOOLPARSER.out.versions)
                                  ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_robust_bias_aware/main.nf:26:18: GRAPHTOOLPARSER is not defined

        .combine(GRAPHTOOLPARSER.out.network.map{ meta, network -> [meta.network_id, meta, network]}, by: 0)
                 ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_rwr/main.nf:5:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/modules/local/graphtoolparser/main.nf'
```
include { GRAPHTOOLPARSER   } from '../../../modules/local/graphtoolparser/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/gt_rwr/main.nf:20:5: GRAPHTOOLPARSER is not defined

    GRAPHTOOLPARSER(ch_network, "rwr")                                      // Convert gt file to rwr specific format
    ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_rwr/main.nf:21:35: GRAPHTOOLPARSER is not defined

    ch_versions = ch_versions.mix(GRAPHTOOLPARSER.out.versions)             // Collect versions
                                  ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_rwr/main.nf:26:18: GRAPHTOOLPARSER is not defined

        .combine(GRAPHTOOLPARSER.out.network.map{ meta, network -> [meta.network_id, meta, network]}, by: 0)
                 ^^^^^^^^^^^^^^^

Error: subworkflows/local/gt_seedperturbation/main.nf:118:18: Unexpected input: '->'
```
            item -> "  " + item.text,
                 ^
```

Error: subworkflows/local/utils_nfcore_diseasemodulediscovery_pipeline/main.nf:357:36: Unexpected input: '='

        logWarnings(monochrome_logs=monochrome_logs, seeds_empty=seeds_empty, module_empty=module_empty, visualization_skipped=visualization_skipped, drugstone_skipped=drugstone_skipped)
                                   ^

Error: workflows/diseasemodulediscovery.nf:10:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/modules/local/inputcheck/main.nf'
```
include { INPUTCHECK                        } from '../modules/local/inputcheck/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:11:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/modules/local/graphtoolparser/main.nf'
```
include { GRAPHTOOLPARSER                   } from '../modules/local/graphtoolparser/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:12:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/modules/local/networkannotation/main.nf'
```
include { NETWORKANNOTATION                 } from '../modules/local/networkannotation/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:30:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/subworkflows/local/gt_seedperturbation/main.nf'
```
include { GT_SEEDPERTURBATION    } from '../subworkflows/local/gt_seedperturbation/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:31:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/subworkflows/local/gt_networkperturbation/main.nf'
```
include { GT_NETWORKPERTURBATION } from '../subworkflows/local/gt_networkperturbation/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:34:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/subworkflows/local/utils_nfcore_diseasemodulediscovery_pipeline/main.nf'
```
include { readTsvAsListOfMaps   } from '../subworkflows/local/utils_nfcore_diseasemodulediscovery_pipeline/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:50:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/subworkflows/local/utils_nfcore_diseasemodulediscovery_pipeline/main.nf'
```
include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_diseasemodulediscovery_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:51:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/diseasemodulediscovery/subworkflows/local/utils_nfcore_diseasemodulediscovery_pipeline/main.nf'
```
include { multiqcTsvFromList     } from '../subworkflows/local/utils_nfcore_diseasemodulediscovery_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:137:5: GRAPHTOOLPARSER is not defined
```
    GRAPHTOOLPARSER(ch_network, 'gt')
    ^^^^^^^^^^^^^^^
```

Error: workflows/diseasemodulediscovery.nf:138:35: GRAPHTOOLPARSER is not defined

    ch_versions = ch_versions.mix(GRAPHTOOLPARSER.out.versions)
                                  ^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:139:26: GRAPHTOOLPARSER is not defined

    ch_network_multiqc = GRAPHTOOLPARSER.out.multiqc
                         ^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:148:21: GRAPHTOOLPARSER is not defined

    ch_network_gt = GRAPHTOOLPARSER.out.network
                    ^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:158:5: INPUTCHECK is not defined
```
    INPUTCHECK(ch_seeds_network)
    ^^^^^^^^^^
```
Error: workflows/diseasemodulediscovery.nf:159:16: INPUTCHECK is not defined
```
    ch_seeds = INPUTCHECK.out.seeds
               ^^^^^^^^^^
```

Error: workflows/diseasemodulediscovery.nf:160:24: INPUTCHECK is not defined

    ch_seeds_multiqc = INPUTCHECK.out.multiqc
                       ^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:173:15: INPUTCHECK is not defined

        .join(INPUTCHECK.out.seeds.map{ meta, seeds -> [meta.id, seeds]}, by: 0, remainder: true)
              ^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:178:18: INPUTCHECK is not defined

    ch_modules = INPUTCHECK.out.seeds_module
                 ^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:216:35: readTsvAsListOfMaps is not defined

        .map{meta, path -> [meta, readTsvAsListOfMaps(path)]}.transpose() // Parse topology information from tsv file
                                  ^^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:232:5: NETWORKANNOTATION is not defined
```
    NETWORKANNOTATION(ch_module_network)
    ^^^^^^^^^^^^^^^^^
```

Error: workflows/diseasemodulediscovery.nf:233:18: NETWORKANNOTATION is not defined

    ch_modules = NETWORKANNOTATION.out.module
                 ^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:234:35: NETWORKANNOTATION is not defined

    ch_versions = ch_versions.mix(NETWORKANNOTATION.out.versions)
                                  ^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:264:13: multiqcTsvFromList is not defined

            multiqcTsvFromList(tsv_data, header)
            ^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:295:17: multiqcTsvFromList is not defined

                multiqcTsvFromList(tsv_data, header)
                ^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:328:17: multiqcTsvFromList is not defined

                multiqcTsvFromList(tsv_data, header)
                ^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:475:13: GT_SEEDPERTURBATION is not defined
```
            GT_SEEDPERTURBATION(
            ^^^^^^^^^^^^^^^^^^^
```

Error: workflows/diseasemodulediscovery.nf:480:43: GT_SEEDPERTURBATION is not defined

            ch_versions = ch_versions.mix(GT_SEEDPERTURBATION.out.versions)
                                          ^^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:482:22: GT_SEEDPERTURBATION is not defined

                .mix(GT_SEEDPERTURBATION.out.multiqc_summary)
                     ^^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:483:22: GT_SEEDPERTURBATION is not defined

                .mix(GT_SEEDPERTURBATION.out.multiqc_jaccard)
                     ^^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:488:13: GT_NETWORKPERTURBATION is not defined
```
            GT_NETWORKPERTURBATION(
            ^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/diseasemodulediscovery.nf:494:43: GT_NETWORKPERTURBATION is not defined

            ch_versions = ch_versions.mix(GT_NETWORKPERTURBATION.out.versions)
                                          ^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:496:22: GT_NETWORKPERTURBATION is not defined

                .mix(GT_NETWORKPERTURBATION.out.multiqc_summary)
                     ^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:497:22: GT_NETWORKPERTURBATION is not defined

                .mix(GT_NETWORKPERTURBATION.out.multiqc_jaccard)
                     ^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/diseasemodulediscovery.nf:617:9: methodsDescriptionText is not defined

        methodsDescriptionText(ch_multiqc_custom_methods_description))
        ^^^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: main.nf:40:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/gt_biopax/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_versions = Channel.empty()                                           // For collecting tool versions
                  ^^^^^^^

Warning: subworkflows/local/gt_biopax/main.nf:24:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
        module = Channel.empty()
                 ^^^^^^^
```

Warning: subworkflows/local/gt_diamond/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_versions = Channel.empty()                                           // For collecting tool versions
                  ^^^^^^^

Warning: subworkflows/local/gt_diamond/main.nf:27:14: Parameter was not used -- prefix with _ to suppress warning

        .map{network_id, seeds_meta, seeds, network_meta, network ->
             ^^^^^^^^^^

Warning: subworkflows/local/gt_domino/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_versions = Channel.empty()                                           // For collecting tool versions
                  ^^^^^^^

Warning: subworkflows/local/gt_domino/main.nf:35:14: Parameter was not used -- prefix with _ to suppress warning

        .map{network_id, seeds_meta, seeds, network_meta, network, slices ->
             ^^^^^^^^^^

Warning: subworkflows/local/gt_firstneighbor/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/gt_firstneighbor/main.nf:20:14: Parameter was not used -- prefix with _ to suppress warning
```
        .map{network_id, seeds_meta, seeds, network_meta, network ->
             ^^^^^^^^^^
```
Warning: subworkflows/local/gt_proximity/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/gt_proximity/main.nf:21:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_sp: it[2].name == "NO_FILE"
                   ^^
```

Warning: subworkflows/local/gt_proximity/main.nf:27:63: Parameter was not used -- prefix with _ to suppress warning

    SHORTEST_PATHS(ch_shortest_paths.no_sp.map{meta, network, sp -> [meta, network]})
                                                              ^^

Warning: subworkflows/local/gt_proximity/main.nf:39:19: Parameter was not used -- prefix with _ to suppress warning

        .multiMap{network_id, meta, module, network, sp ->
                  ^^^^^^^^^^

Warning: subworkflows/local/gt_robust/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/gt_robust/main.nf:25:14: Parameter was not used -- prefix with _ to suppress warning

        .map{network_id, seeds_meta, seeds, network_meta, network ->
             ^^^^^^^^^^

Warning: subworkflows/local/gt_robust_bias_aware/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/gt_robust_bias_aware/main.nf:27:14: Parameter was not used -- prefix with _ to suppress warning
```
        .map{network_id, seeds_meta, seeds, network_meta, network ->
             ^^^^^^^^^^
```

Warning: subworkflows/local/gt_rwr/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_versions = Channel.empty()                                           // For collecting tool versions
                  ^^^^^^^

Warning: subworkflows/local/gt_rwr/main.nf:27:14: Parameter was not used -- prefix with _ to suppress warning

        .map{network_id, seeds_meta, seeds, network_meta, network ->
             ^^^^^^^^^^

Warning: subworkflows/local/networkexpansion/main.nf:21:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    diamond_n = Channel.value(params.diamond_n)
                ^^^^^^^
```
Warning: subworkflows/local/networkexpansion/main.nf:22:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    diamond_alpha = Channel.value(params.diamond_alpha)
                    ^^^^^^^
```
Warning: subworkflows/local/networkexpansion/main.nf:24:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    rwr_scaling = Channel.value(params.rwr_scaling).map{it ? 1 : 0}
                  ^^^^^^^
```
Warning: subworkflows/local/networkexpansion/main.nf:24:57: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    rwr_scaling = Channel.value(params.rwr_scaling).map{it ? 1 : 0}
                                                        ^^
```
Warning: subworkflows/local/networkexpansion/main.nf:25:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    rwr_symmetrical = Channel.value(params.rwr_symmetrical).map{it ? 1 : 0}
                      ^^^^^^^
```

Warning: subworkflows/local/networkexpansion/main.nf:25:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

    rwr_symmetrical = Channel.value(params.rwr_symmetrical).map{it ? 1 : 0}
                                                                ^^

Warning: subworkflows/local/networkexpansion/main.nf:26:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
    rwr_r = Channel.value(params.rwr_r)
            ^^^^^^^
```
Warning: subworkflows/local/networkexpansion/main.nf:28:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    id_space = Channel.value(params.id_space)
               ^^^^^^^
```
Warning: subworkflows/local/networkexpansion/main.nf:31:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/networkexpansion/main.nf:32:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_modules  = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/networkexpansion/main.nf:33:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_raw_modules = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/networkexpansion/main.nf:76:14: Parameter was not used -- prefix with _ to suppress warning
```
        .map{seeds_id, network_id, meta, module, seeds ->
             ^^^^^^^^
```

Warning: subworkflows/local/networkexpansion/main.nf:76:24: Parameter was not used -- prefix with _ to suppress warning

        .map{seeds_id, network_id, meta, module, seeds ->
                       ^^^^^^^^^^

Warning: subworkflows/local/networkexpansion/main.nf:86:14: Parameter was not used -- prefix with _ to suppress warning
```
        .map{network_id, meta, module, seeds, network ->
             ^^^^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:121:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    id_space = Channel.value(params.id_space)
               ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:122:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    validate_online = Channel.value(params.validate_online)
                      ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:129:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:130:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:131:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_seeds_empty_status = Channel.empty()
                            ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:132:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_module_empty_status = Channel.empty()
                             ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:133:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_visualization_skipped_status = Channel.empty()
                                      ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:134:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_drugstone_skipped_status = Channel.empty()
                                  ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:140:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ meta, path -> path }
              ^^^^
```
Warning: workflows/diseasemodulediscovery.nf:156:14: Parameter was not used -- prefix with _ to suppress warning
```
        .map{key, meta, seeds, network -> [meta, seeds, network]}
             ^^^
```
Warning: workflows/diseasemodulediscovery.nf:161:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ meta, path -> path }
              ^^^^
```
Warning: workflows/diseasemodulediscovery.nf:172:20: Parameter was not used -- prefix with _ to suppress warning
```
        .map{meta, seeds, network -> meta.id}
                   ^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:172:27: Parameter was not used -- prefix with _ to suppress warning
```
        .map{meta, seeds, network -> meta.id}
                          ^^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:204:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ meta, path -> path }
              ^^^^
```
Warning: workflows/diseasemodulediscovery.nf:230:14: Parameter was not used -- prefix with _ to suppress warning
```
        .map{newtork_id, meta, module, network -> [meta, module, network]}
             ^^^^^^^^^^
```

Warning: workflows/diseasemodulediscovery.nf:240:23: Parameter was not used -- prefix with _ to suppress warning

        .filter{meta, module -> meta.nodes > 0} // Filter out empty modules
                      ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:246:24: Parameter was not used -- prefix with _ to suppress warning
```
        .branch{ meta, module ->
                       ^^^^^^
```

Warning: workflows/diseasemodulediscovery.nf:254:58: Parameter was not used -- prefix with _ to suppress warning

        .mix(ch_modules_empty_not_empty.empty.map {meta, module -> [meta.id, true] })
                                                         ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:255:62: Parameter was not used -- prefix with _ to suppress warning

        .mix(ch_modules_empty_not_empty.not_empty.map {meta, module -> [meta.id, false] })
                                                             ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:260:21: Parameter was not used -- prefix with _ to suppress warning
```
        .map {meta, module -> "$meta.id\t$meta.nodes" }
                    ^^^^^^
```

Warning: workflows/diseasemodulediscovery.nf:278:28: Parameter was not used -- prefix with _ to suppress warning

            .branch {meta, module ->
                           ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:285:57: Parameter was not used -- prefix with _ to suppress warning

            .mix(ch_visualization_input.fail.map {meta, module -> [meta.id, true] })
                                                        ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:286:57: Parameter was not used -- prefix with _ to suppress warning

            .mix(ch_visualization_input.pass.map {meta, module -> [meta.id, false] })
                                                        ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:291:25: Parameter was not used -- prefix with _ to suppress warning
```
            .map {meta, module -> "$meta.id\t$meta.nodes" }
                        ^^^^^^
```

Warning: workflows/diseasemodulediscovery.nf:311:28: Parameter was not used -- prefix with _ to suppress warning

            .branch {meta, module ->
                           ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:318:56: Parameter was not used -- prefix with _ to suppress warning

        .mix(ch_drugstone_export_input.fail.map {meta, module -> [meta.id, true] })
                                                       ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:319:56: Parameter was not used -- prefix with _ to suppress warning

        .mix(ch_drugstone_export_input.pass.map {meta, module -> [meta.id, false] })
                                                       ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:324:25: Parameter was not used -- prefix with _ to suppress warning
```
            .map {meta, module -> "$meta.id\t$meta.nodes" }
                        ^^^^^^
```
Warning: workflows/diseasemodulediscovery.nf:340:19: Parameter was not used -- prefix with _ to suppress warning
```
            .map{ meta, path -> path }
                  ^^^^
```

Warning: workflows/diseasemodulediscovery.nf:394:27: Parameter was not used -- prefix with _ to suppress warning

                .multiMap{key, meta, nodes, network ->
                          ^^^

Warning: workflows/diseasemodulediscovery.nf:416:27: Parameter was not used -- prefix with _ to suppress warning

                .multiMap{key, meta, nodes, network ->
                          ^^^

Warning: workflows/diseasemodulediscovery.nf:425:27: Parameter was not used -- prefix with _ to suppress warning
```
                    .map{ meta, path -> path }
                          ^^^^
```

Warning: workflows/diseasemodulediscovery.nf:438:36: Parameter was not used -- prefix with _ to suppress warning

                    .filter{ meta, nodes -> meta.amim != "no_tool" } // Filter out no_tool modules
                                   ^^^^^

Warning: workflows/diseasemodulediscovery.nf:441:31: Parameter was not used -- prefix with _ to suppress warning

                    .multiMap{key, meta, nodes, network ->
                              ^^^

Warning: workflows/diseasemodulediscovery.nf:450:27: Parameter was not used -- prefix with _ to suppress warning
```
                    .map{ meta, path -> path }
                          ^^^^
```

Warning: workflows/diseasemodulediscovery.nf:476:42: Parameter was not used -- prefix with _ to suppress warning

                ch_modules.filter{ meta, path -> meta.amim != "no_tool" }, // Filter out no_tool modules
                                         ^^^^

Warning: workflows/diseasemodulediscovery.nf:489:42: Parameter was not used -- prefix with _ to suppress warning

                ch_modules.filter{ meta, path -> meta.amim != "no_tool" }, // Filter out no_tool modules
                                         ^^^^

Warning: workflows/diseasemodulediscovery.nf:513:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_algorithms_drugs = Channel
                              ^^^^^^^
```

Warning: workflows/diseasemodulediscovery.nf:523:28: Parameter was not used -- prefix with _ to suppress warning

            .branch {meta, module ->
                           ^^^^^^

Warning: workflows/diseasemodulediscovery.nf:537:32: The use of Channel to access channel factories is deprecated -- use channel instead

        includeIndirectDrugs = Channel.value(params.includeIndirectDrugs).map{it ? 1 : 0}
                               ^^^^^^^

Warning: workflows/diseasemodulediscovery.nf:537:79: Implicit closure parameter is deprecated, declare an explicit parameter instead

        includeIndirectDrugs = Channel.value(params.includeIndirectDrugs).map{it ? 1 : 0}
                                                                              ^^

Warning: workflows/diseasemodulediscovery.nf:538:35: The use of Channel to access channel factories is deprecated -- use channel instead

        includeNonApprovedDrugs = Channel.value(params.includeNonApprovedDrugs).map{it ? 1 : 0}
                                  ^^^^^^^

Warning: workflows/diseasemodulediscovery.nf:538:85: Implicit closure parameter is deprecated, declare an explicit parameter instead

        includeNonApprovedDrugs = Channel.value(params.includeNonApprovedDrugs).map{it ? 1 : 0}
                                                                                    ^^

Warning: workflows/diseasemodulediscovery.nf:545:29: Parameter was not used -- prefix with _ to suppress warning

                .map{ meta, algorithm, drug_predictions -> [meta, drug_predictions] }
                            ^^^^^^^^^

Warning: workflows/diseasemodulediscovery.nf:546:32: Parameter was not used -- prefix with _ to suppress warning

                .filter{ meta, drug_predictions -> meta.nodes <= params.visualization_max_nodes }       // Filter out modules with too many nodes
                               ^^^^^^^^^^^^^^^^

Warning: workflows/diseasemodulediscovery.nf:549:22: Parameter was not used -- prefix with _ to suppress warning

                .map{module_id, meta, drug_predictions, module -> [meta, module, drug_predictions] }    // Format for visualization
                     ^^^^^^^^^

Warning: workflows/diseasemodulediscovery.nf:569:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def topic_versions = Channel.topic("versions")
                         ^^^^^^^
```

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