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panoramaseq_lint.md

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Nextflow lint results

  • Generated: 2026-01-16T10:25:23.970139803Z
  • Nextflow version: 25.12.0-edge
  • Summary: 6 errors, 16 warnings

❌ Errors

  • Error: nextflow.config:270:35: manifest is not defined

    \033[0;35m  nf-core/panoramaseq ${manifest.version}\033[0m
                                  ^^^^^^^^

  • Error: nextflow.config:273:26: manifest is not defined

            afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                         ^^^^^^^^

  • Error: nextflow.config:273:69: manifest is not defined

            afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                    ^^^^^^^^

  • Error: nextflow.config:273:186: manifest is not defined

            afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                                                                         ^^^^^^^^

  • Error: nextflow.config:282:22: validation is not defined

            beforeText = validation.help.beforeText
                     ^^^^^^^^^^

  • Error: nextflow.config:283:21: validation is not defined

            afterText = validation.help.afterText
                    ^^^^^^^^^^

⚠️ Warnings

  • Warning: nextflow.config:273:129: Implicit closure parameter is deprecated, declare an explicit parameter instead

            afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                ^^

  • Warning: subworkflows/local/utils_nfcore_panoramaseq_pipeline/main.nf:31:5: Parameter was not used -- prefix with _ to suppress warning

        monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_panoramaseq_pipeline/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning

        input             //  string: Path to input samplesheet
    ^^^^^

  • Warning: subworkflows/local/utils_nfcore_panoramaseq_pipeline/main.nf:38:19: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_versions = Channel.empty()
                  ^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_panoramaseq_pipeline/main.nf:75:5: The use of Channel to access channel factories is deprecated -- use channel instead

        Channel
    ^^^^^^^

  • Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:98: The use of Channel to access channel factories is deprecated -- use channel instead

        return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
                                                                                                 ^^^^^^^

  • Warning: workflows/panoramaseq.nf:25:19: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_versions = Channel.empty()
                  ^^^^^^^

  • Warning: workflows/panoramaseq.nf:26:24: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_files = Channel.empty()
                       ^^^^^^^

  • Warning: workflows/panoramaseq.nf:33:68: 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/panoramaseq.nf:51:32: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^

  • Warning: workflows/panoramaseq.nf:54:9: The use of Channel to access channel factories is deprecated -- use channel instead

            Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^

  • Warning: workflows/panoramaseq.nf:55:9: The use of Channel to access channel factories is deprecated -- use channel instead

            Channel.empty()
        ^^^^^^^

  • Warning: workflows/panoramaseq.nf:57:9: The use of Channel to access channel factories is deprecated -- use channel instead

            Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^

  • Warning: workflows/panoramaseq.nf:58:9: The use of Channel to access channel factories is deprecated -- use channel instead

            Channel.empty()
        ^^^^^^^

  • Warning: workflows/panoramaseq.nf:62:27: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^

  • Warning: workflows/panoramaseq.nf:68:45: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_methods_description                = Channel.value(
                                            ^^^^^^^