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isoseq_lint.md

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Nextflow lint results

  • Generated: 2026-06-16T20:27:16.417909918Z
  • Nextflow version: 26.04.3
  • Summary: 28 warnings

⚠️ Warnings

  • Warning: main.nf:57:5: Emit name should be omitted when there is only one emit

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

  • Warning: modules/local/gstama/filelist/main.nf:20:9: Variable was declared but not used

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

  • Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used

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

  • Warning: modules/nf-core/isoseq/refine/main.nf:44:9: Variable was declared but not used

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

  • Warning: modules/nf-core/isoseq/refine/main.nf:45:9: Variable was declared but not used

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

  • Warning: modules/nf-core/minimap2/align/main.nf:67:9: Variable was declared but not used

        def target = reference ?: (bam_input ? error("BAM input requires reference") : reads)
        ^^^^^^

  • Warning: modules/nf-core/pbccs/main.nf:47:9: Variable was declared but not used

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

  • Warning: modules/nf-core/pbccs/main.nf:48:9: Variable was declared but not used

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

  • Warning: subworkflows/local/chunker/main.nf:39:16: Variable was declared but not used

            .set { fastas }
               ^^^^^^

  • Warning: subworkflows/local/chunker/main.nf:42:5: Emit name should be omitted when there is only one emit

        fastas
    ^^^^^^

  • Warning: subworkflows/local/set_chunk_num_channel/main.nf:15:16: Variable was declared but not used

            .set { chunk_num }
               ^^^^^^^^^

  • Warning: subworkflows/local/set_chunk_num_channel/main.nf:18:5: Emit name should be omitted when there is only one emit

        chunk_num
    ^^^^^^^^^

  • Warning: subworkflows/local/set_value_channel/main.nf:15:20: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .map { it[1] }
                   ^^

  • Warning: subworkflows/local/set_value_channel/main.nf:26:5: Emit name should be omitted when there is only one emit

        data // channel: [ file(infile) ]
    ^^^^

  • Warning: subworkflows/local/utils_nfcore_isoseq_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_isoseq_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_isoseq_pipeline/main.nf:67:144: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

  • 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_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: 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/isoseq.nf:206:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

        GSTAMA_MERGE(ch_tmerge_in.map { [ it[0], it[1] ] }, ch_tmerge_in.map { it[2] }) // Merge all bed files from one sample into a uniq bed file
                                      ^^

  • Warning: workflows/isoseq.nf:206:46: Implicit closure parameter is deprecated, declare an explicit parameter instead

        GSTAMA_MERGE(ch_tmerge_in.map { [ it[0], it[1] ] }, ch_tmerge_in.map { it[2] }) // Merge all bed files from one sample into a uniq bed file
                                             ^^

  • Warning: workflows/isoseq.nf:206:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

        GSTAMA_MERGE(ch_tmerge_in.map { [ it[0], it[1] ] }, ch_tmerge_in.map { it[2] }) // Merge all bed files from one sample into a uniq bed file
                                                                           ^^

  • Warning: workflows/isoseq.nf:283:75: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(PBCCS.out.report_json.collect{it[1]}.ifEmpty([]))
                                                                          ^^

  • Warning: workflows/isoseq.nf:284:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(LIMA.out.summary.collect{it[1]}.ifEmpty([]))
                                                                     ^^

  • Warning: workflows/isoseq.nf:285:69: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(LIMA.out.counts.collect{it[1]}.ifEmpty([]))
                                                                    ^^