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isoseq_lint.md

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Nextflow lint results

  • Generated: 2026-01-16T17:21:26.307650683Z
  • Nextflow version: 25.12.0-edge
  • Summary: 31 warnings

⚠️ Warnings

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

                .map { it[1] }
                   ^^

  • 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:42:19: The use of Channel to access channel factories is deprecated -- use channel instead

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

  • 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/local/utils_nfcore_isoseq_pipeline/main.nf:104:9: The use of Channel to access channel factories is deprecated -- use channel instead

            Channel
        ^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf:106:45: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .flatMap { create_pbccs_channel(it, params.chunk) }
                                            ^^

  • Warning: subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf:111:9: The use of Channel to access channel factories is deprecated -- use channel instead

            Channel
        ^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf:113:45: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .flatMap { create_reads_channel(it) }
                                            ^^

  • Warning: subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf:121:28: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    def chk = (it[1] =~ /(chunk\.\d+)\.gz/)[ 0 ][ 1 ]
                           ^^

  • Warning: subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf:122:33: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    def id_former = it[0].id
                                ^^

  • Warning: subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf:123:33: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    def id_new    = it[0].id + "." + chk
                                ^^

  • Warning: subworkflows/local/utils_nfcore_isoseq_pipeline/main.nf:124:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    [ [ id:id_new, id_former:id_former ] , it[1] ]
                                                       ^^

  • 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/isoseq.nf:142:39: Parameter was not used -- prefix with _ to suppress warning

                .map { meta1, pickle, db, meta2, reads -> [meta1, pickle, db] }
                                      ^^^^^

  • Warning: workflows/isoseq.nf:142:46: Parameter was not used -- prefix with _ to suppress warning

                .map { meta1, pickle, db, meta2, reads -> [meta1, pickle, db] }
                                             ^^^^^

  • Warning: workflows/isoseq.nf:162:22: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [ [id:it[0].id_former], it[1] ] }
                     ^^

  • Warning: workflows/isoseq.nf:162:40: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [ [id:it[0].id_former], it[1] ] }
                                       ^^

  • Warning: workflows/isoseq.nf:177:39: 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:177:46: 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:177:76: 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:258:79: 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:259:74: 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:260:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

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