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genomeskim_lint.md

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Nextflow lint results

  • Generated: 2026-01-16T10:21:32.133019559Z
  • Nextflow version: 25.12.0-edge
  • Summary: 40 errors, 13 warnings

❌ Errors

  • Error: conf/base.config:14:16: check_max is not defined

        cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
               ^^^^^^^^^

  • Error: conf/base.config:15:16: check_max is not defined

        memory = { check_max( 6.GB * task.attempt, 'memory' ) }
               ^^^^^^^^^

  • Error: conf/base.config:16:16: check_max is not defined

        time   = { check_max( 4.h  * task.attempt, 'time'   ) }
               ^^^^^^^^^

  • Error: conf/base.config:30:20: check_max is not defined

            cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

  • Error: conf/base.config:31:20: check_max is not defined

            memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

  • Error: conf/base.config:32:20: check_max is not defined

            time   = { check_max( 4.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

  • Error: conf/base.config:35:20: check_max is not defined

            cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

  • Error: conf/base.config:36:20: check_max is not defined

            memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

  • Error: conf/base.config:37:20: check_max is not defined

            time   = { check_max( 8.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

  • Error: conf/base.config:40:20: check_max is not defined

            cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

  • Error: conf/base.config:41:20: check_max is not defined

            memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

  • Error: conf/base.config:42:20: check_max is not defined

            time   = { check_max( 16.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

  • Error: conf/base.config:45:20: check_max is not defined

            time   = { check_max( 20.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

  • Error: conf/base.config:48:20: check_max is not defined

            memory = { check_max( 200.GB * task.attempt, 'memory' ) }
                   ^^^^^^^^^

  • Error: main.nf:20:16: WorkflowMain is not defined

    params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
               ^^^^^^^^^^^^

  • Error: main.nf:28:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    WorkflowMain.initialise(workflow, params, log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: main.nf:28:1: WorkflowMain is not defined

    WorkflowMain.initialise(workflow, params, log)
^^^^^^^^^^^^

  • Error: nextflow.config:61:5: Unexpected input: 'includeConfig'

        includeConfig "${params.custom_config_base}/nfcore_custom.config"
    ^

  • Error: workflows/genomeskim.nf:7:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:7:22: NfcoreSchema is not defined

    def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
                     ^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:10:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    WorkflowGenomeskim.initialise(params, log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:10:1: WorkflowGenomeskim is not defined

    WorkflowGenomeskim.initialise(params, log)
^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:14:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:15:1: for loops are no longer supported

    for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
^^^

  • Error: workflows/genomeskim.nf:15:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:15:6: param is not defined

    for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
     ^^^^^

  • Error: workflows/genomeskim.nf:15:40: param is not defined

    for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
                                       ^^^^^^^

  • Error: workflows/genomeskim.nf:15:55: param is not defined

    for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
                                                      ^^^^^

  • Error: workflows/genomeskim.nf:18:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:26:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:27:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:60:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    def multiqc_report = []
^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:70:9: ch_input is not defined

            ch_input
        ^^^^^^^^

  • Error: workflows/genomeskim.nf:89:27: WorkflowGenomeskim is not defined

        workflow_summary    = WorkflowGenomeskim.paramsSummaryMultiqc(workflow, summary_params)
                          ^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:89:77: summary_params is not defined

        workflow_summary    = WorkflowGenomeskim.paramsSummaryMultiqc(workflow, summary_params)
                                                                            ^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:93:58: ch_multiqc_config is not defined

        ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
                                                         ^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:94:45: ch_multiqc_custom_config is not defined

        ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
                                            ^^^^^^^^^^^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:112:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

    workflow.onComplete {
^

  • Error: workflows/genomeskim.nf:114:9: NfcoreTemplate is not defined

            NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
        ^^^^^^^^^^^^^^

  • Error: workflows/genomeskim.nf:116:5: NfcoreTemplate is not defined

        NfcoreTemplate.summary(workflow, params, log)
    ^^^^^^^^^^^^^^

⚠️ Warnings

  • Warning: modules/nf-core/modules/custom/dumpsoftwareversions/main.nf:22:9: Variable was declared but not used

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

  • Warning: subworkflows/local/input_check.nf:15:37: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { create_fastq_channel(it) }
                                    ^^

  • Warning: workflows/genomeskim.nf:18:21: Variable was declared but not used

    if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
                    ^^^^^^^^

  • Warning: workflows/genomeskim.nf:26:1: Variable was declared but not used

    ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
^^^^^^^^^^^^^^^^^

  • Warning: workflows/genomeskim.nf:27:1: Variable was declared but not used

    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: workflows/genomeskim.nf:27:52: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
                                                   ^^^^^^^

  • Warning: workflows/genomeskim.nf:27:94: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
                                                                                             ^^^^^^^

  • Warning: workflows/genomeskim.nf:64:19: The use of Channel to access channel factories is deprecated -- use channel instead

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

  • Warning: workflows/genomeskim.nf:90:27: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_workflow_summary = Channel.value(workflow_summary)
                          ^^^^^^^

  • Warning: workflows/genomeskim.nf:92:24: The use of Channel to access channel factories is deprecated -- use channel instead

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

  • Warning: workflows/genomeskim.nf:93:45: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
                                            ^^^^^^^

  • Warning: workflows/genomeskim.nf:97:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

  • Warning: workflows/genomeskim.nf:102:5: Variable was declared but not used

        multiqc_report = MULTIQC.out.report.toList()
    ^^^^^^^^^^^^^^