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drugresponseeval_lint.md

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Nextflow lint results

  • Generated: 2026-01-23T00:19:41.883422820Z
  • Nextflow version: 25.12.0-edge
  • Summary: 7 errors, 29 warnings

❌ Errors

  • Error: modules/nf-core/custom/dumpsoftwareversions/main.nf:1:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    def deprecation_message = """
^^^

  • Error: modules/nf-core/custom/dumpsoftwareversions/main.nf:30:18: deprecation_message is not defined

        assert true: deprecation_message
                 ^^^^^^^^^^^^^^^^^^^

  • Error: workflows/drugresponseeval.nf:24:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    def test_modes = params.test_mode.split(",")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/drugresponseeval.nf:25:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    def randomizations = params.randomization_mode.split(",")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/drugresponseeval.nf:48:9: test_modes is not defined

            test_modes,
        ^^^^^^^^^^

  • Error: workflows/drugresponseeval.nf:59:9: randomizations is not defined

            randomizations,
        ^^^^^^^^^^^^^^

  • Error: workflows/drugresponseeval.nf:64:9: test_modes is not defined

            test_modes,
        ^^^^^^^^^^

⚠️ Warnings

  • Warning: conf/modules.config:65:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:73:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:81:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:89:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:97:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:105:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:114:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:133:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:159:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:205:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:213:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: conf/modules.config:239:23: Parameter was not used -- prefix with _ to suppress warning

                saveAs: { filename -> null }
                      ^^^^^^^^

  • Warning: modules/nf-core/custom/dumpsoftwareversions/main.nf:1:5: Variable was declared but not used

    def deprecation_message = """
    ^^^^^^^^^^^^^^^^^^^

  • Warning: modules/nf-core/custom/dumpsoftwareversions/main.nf:31:9: Variable was declared but not used

        def args = task.ext.args ?: ''
        ^^^^

  • Warning: modules/nf-core/unzip/main.nf:38:9: Variable was declared but not used

        def args = task.ext.args ?: ''
        ^^^^

  • Warning: subworkflows/local/model_testing/main.nf:63:31: Parameter was not used -- prefix with _ to suppress warning

                            .map{ model_class, model_name, rand_file -> [model_name, rand_file] }
                              ^^^^^^^^^^^

  • Warning: subworkflows/local/model_testing/main.nf:125:36: Parameter was not used -- prefix with _ to suppress warning

                                .map { model_class, model_name, train_ds, val_ds, es_ds ->
                                   ^^^^^^^^^^^

  • Warning: subworkflows/local/model_testing/main.nf:145:47: Parameter was not used -- prefix with _ to suppress warning

                                .map{ model_name, final_constant, test_mode, best_hpam_combi ->
                                              ^^^^^^^^^^^^^^

  • Warning: subworkflows/local/model_testing/main.nf:158:49: Parameter was not used -- prefix with _ to suppress warning

                            .map{ test_mode, model, pred_file -> [test_mode, model.split("\\.")[0]] }
                                                ^^^^^^^^^

  • Warning: subworkflows/local/run_cv/main.nf:54:43: Parameter was not used -- prefix with _ to suppress warning

                                    .filter { dataset_name, dataset_path ->
                                          ^^^^^^^^^^^^

  • Warning: subworkflows/local/run_cv/main.nf:57:40: Parameter was not used -- prefix with _ to suppress warning

                                    .map { dataset_name, dataset_path ->
                                       ^^^^^^^^^^^^

  • Warning: subworkflows/local/run_cv/main.nf:62:43: Parameter was not used -- prefix with _ to suppress warning

                                    .filter { dataset_name, dataset_path ->
                                          ^^^^^^^^^^^^

  • Warning: subworkflows/local/run_cv/main.nf:131:16: Parameter was not used -- prefix with _ to suppress warning

            .map { model_class, model_name, hpam_combis -> [model_name, hpam_combis] }
               ^^^^^^^^^^^

  • Warning: subworkflows/local/run_cv/main.nf:139:16: Parameter was not used -- prefix with _ to suppress warning

            .map { model_class, model_name, test_mode, split -> [model_name, test_mode, split] }
               ^^^^^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_drugresponseeval_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_drugresponseeval_pipeline/main.nf:129:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_models = channel.from(models.split(',').collect { it.trim() })
                                                         ^^

  • Warning: workflows/drugresponseeval.nf:24:5: Variable was declared but not used

    def test_modes = params.test_mode.split(",")
    ^^^^^^^^^^

  • Warning: workflows/drugresponseeval.nf:25:5: Variable was declared but not used

    def randomizations = params.randomization_mode.split(",")
    ^^^^^^^^^^^^^^

  • Warning: workflows/drugresponseeval.nf:96:17: Variable was declared but not used

            ).set { ch_collated_versions }
                ^^^^^^^^^^^^^^^^^^^^