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dartseq_lint.md

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Nextflow lint results

  • Generated: 2026-06-13T00:45:29.579422530Z
  • Nextflow version: 26.04.3
  • Summary: 23 warnings

⚠️ Warnings

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

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

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

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

  • 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_nfschema_plugin/main.nf:72:5: Emit name should be omitted when there is only one emit

        dummy_emit = true
    ^^^^^^^^^^^^^^^

  • Warning: workflows/dartseq.nf:54:68: 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/dartseq.nf:69:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.html.collect{it[1]})
                                                                       ^^

  • Warning: workflows/dartseq.nf:70:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.json.collect{it[1]})
                                                                       ^^

  • Warning: workflows/dartseq.nf:71:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.log.collect{it[1]})
                                                                      ^^

  • Warning: workflows/dartseq.nf:77:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(TRIMGALORE.out.zip.collect{it[1]})
                                                                           ^^

  • Warning: workflows/dartseq.nf:78:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(TRIMGALORE.out.html.collect{it[1]})
                                                                            ^^

  • Warning: workflows/dartseq.nf:79:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(TRIMGALORE.out.log.collect{it[1]})
                                                                           ^^

  • Warning: workflows/dartseq.nf:88:35: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_fasta = params.fasta ? Channel.value([ [ id: 'fasta' ], file(params.fasta, checkIfExists: true) ]) : channel.empty()
                                  ^^^^^^^

  • Warning: workflows/dartseq.nf:89:31: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_gtf = params.gtf ? Channel.value([ [ id: 'gtf' ], file(params.gtf, checkIfExists: true) ]) : channel.empty()
                              ^^^^^^^

  • Warning: workflows/dartseq.nf:100:19: The use of Channel to access channel factories is deprecated -- use channel instead

                    ? Channel.value([ [ id: 'star_index' ], file(params.star_index, checkIfExists: true) ])
                  ^^^^^^^

  • Warning: workflows/dartseq.nf:117:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_multiqc_files = ch_multiqc_files.mix(STAR_ALIGN.out.log_final.collect{it[1]})
                                                                                     ^^

  • Warning: workflows/dartseq.nf:129:19: The use of Channel to access channel factories is deprecated -- use channel instead

                    ? Channel.value([ [ id: 'hisat2_index' ], file(params.hisat2_index, checkIfExists: true) ])
                  ^^^^^^^

  • Warning: workflows/dartseq.nf:133:19: The use of Channel to access channel factories is deprecated -- use channel instead

                    ? Channel.value([ [ id: 'splicesites' ], file(params.hisat2_splicesites, checkIfExists: true) ])
                  ^^^^^^^

  • Warning: workflows/dartseq.nf:164:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_multiqc_files = ch_multiqc_files.mix(HISAT2_ALIGN.out.summary.collect{it[1]})
                                                                                     ^^

  • Warning: workflows/dartseq.nf:169:17: The use of Channel to access channel factories is deprecated -- use channel instead

                    Channel.value([ [ id: 'no_fasta' ], [], [] ]),
                ^^^^^^^

  • Warning: workflows/dartseq.nf:383:26: The use of Channel to access channel factories is deprecated -- use channel instead

        def topic_versions = Channel.topic("versions")
                         ^^^^^^^