Nextflow lint results

Generated: 2026-01-16T10:27:12.824567503Z
Nextflow version: 25.12.0-edge
Summary: 53 errors, 49 warnings

❌ Errors

Error: conf/base.config:13:16: check_max is not defined

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

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

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

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

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

Error: conf/base.config:28:20: check_max is not defined

        cpus   = { check_max( 1                  , 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:29:20: check_max is not defined

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

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

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

Error: conf/base.config:33:20: check_max is not defined

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

Error: conf/base.config:34:20: check_max is not defined

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

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

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

Error: conf/base.config:38:20: check_max is not defined

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

Error: conf/base.config:39:20: check_max is not defined

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

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

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

Error: conf/base.config:43:20: check_max is not defined

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

Error: conf/base.config:44:20: check_max is not defined

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

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

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

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

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

Error: conf/base.config:51:20: check_max is not defined

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

Error: main.nf:34:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (!params.fasta) {
^
```

Error: modules/local/insilicoseq/generate/main.nf:26:9: input_format is already declared

    def input_format  = input_format == "genomes" ? "--genomes": "--draft"
        ^^^^^^^^^^^^

Error: modules/local/uncompress_fasta/main.nf:2:10: file is not defined
```
    tag "$file"
         ^^^^^
```

Error: modules/nf-core/multiqc/main.nf:28:31: Unexpected input: '/'

    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
                              ^

Error: nextflow.config:123:5: Unexpected input: 'includeConfig'

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

Error: subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf:14:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/readsimulator/subworkflows/nf-core/utils_nextflow_pipeline/main.nf'
```
include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf:47:5: UTILS_NEXTFLOW_PIPELINE is not defined
```
    UTILS_NEXTFLOW_PIPELINE (
    ^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:111:14: Unexpected input: 'i'
```
    for (int i = 0; i < n - 1; i++) {
             ^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:5:1: Groovy import declarations are not supported -- use fully-qualified name inline instead
```
import org.yaml.snakeyaml.Yaml
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:6:1: Groovy import declarations are not supported -- use fully-qualified name inline instead
```
import nextflow.extension.FilesEx
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:37:5: valid_config was assigned but not declared
```
    valid_config = true
    ^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:45:9: valid_config was assigned but not declared
```
        valid_config = false
        ^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:47:12: valid_config is not defined
```
    return valid_config
           ^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:99:17: Yaml is not defined
```
    Yaml yaml = new Yaml()
                ^^^^^^^^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:100:5: versions was assigned but not declared

    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
    ^^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:27: versions is not defined
```
    return yaml.dumpAsMap(versions).trim()
                          ^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:131:5: for loops are no longer supported
```
    for (group in summary_params.keySet()) {
    ^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:131:10: group is not defined
```
    for (group in summary_params.keySet()) {
         ^^^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:132:47: group is not defined

        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
                                              ^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:134:68: group is not defined

            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
                                                                   ^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:136:13: for loops are no longer supported
```
            for (param in group_params.keySet()) {
            ^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:136:18: param is not defined

            for (param in group_params.keySet()) {
                 ^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:137:49: param is not defined

                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
                                                ^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:137:89: param is not defined

                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
                                                                                        ^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:284:5: for loops are no longer supported
```
    for (group in summary_params.keySet()) {
    ^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:284:10: group is not defined
```
    for (group in summary_params.keySet()) {
         ^^^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:285:34: group is not defined

        summary << summary_params[group]
                                 ^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:344:42: GroovyException is not defined

            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
                                         ^^^^^^^^^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:361:5: FilesEx is not defined

    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
    ^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:367:5: FilesEx is not defined

    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
    ^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:392:5: for loops are no longer supported
```
    for (group in summary_params.keySet()) {
    ^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:392:10: group is not defined
```
    for (group in summary_params.keySet()) {
         ^^^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:393:34: group is not defined

        summary << summary_params[group]
                                 ^^^^^^^

Error: workflows/readsimulator/main.nf:8:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/readsimulator/modules/nf-core/multiqc/main.nf'
```
include { MULTIQC                     } from '../../modules/nf-core/multiqc/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/readsimulator/main.nf:197:5: MULTIQC is not defined
```
    MULTIQC (
    ^^^^^^^
```

Error: workflows/readsimulator/main.nf:207:23: MULTIQC is not defined

    multiqc_report  = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
                      ^^^^^^^

⚠️ Warnings

Warning: main.nf:35:5: Params should be declared at the top-level (i.e. outside the workflow)
```
    params.fasta = getGenomeAttribute('fasta')
    ^^^^^^
```

Warning: modules/local/custom/create_samplesheet/main.nf:26:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

    samplesheet  = pipeline_map.keySet().collect{ '"' + it + '"'}.join(",") + '\n'
                                                        ^^

Warning: modules/local/custom/create_samplesheet/main.nf:27:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

    samplesheet += pipeline_map.values().collect{ '"' + it + '"'}.join(",")
                                                        ^^

Warning: modules/local/custom/merge_samplesheets/main.nf:20:9: Variable was declared but not used
```
    def args    = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/fastqc/main.nf:27:48: Parameter was not used -- prefix with _ to suppress warning

    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
                                               ^^^^^^^^

Warning: modules/nf-core/ncbigenomedownload/main.nf:37:9: Variable was declared but not used

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

Warning: subworkflows/local/amplicon_workflow.nf:16:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_ref_fasta = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/amplicon_workflow.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/amplicon_workflow.nf:47:13: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it = [ it[2], it[1] ]
            ^^
```
Warning: subworkflows/local/amplicon_workflow.nf:47:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it = [ it[2], it[1] ]
                   ^^
```
Warning: subworkflows/local/amplicon_workflow.nf:47:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it = [ it[2], it[1] ]
                          ^^
```
Warning: subworkflows/local/target_capture_workflow.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/target_capture_workflow.nf:26:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_zip_file = Channel.fromPath(params.probe_ref_db[params.probe_ref_name]["url"])
                      ^^^^^^^
```
Warning: subworkflows/local/target_capture_workflow.nf:93:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_capsim_input = ch_meta_fasta.map { it = it[1] }
                                          ^^
```
Warning: subworkflows/local/target_capture_workflow.nf:93:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_capsim_input = ch_meta_fasta.map { it = it[1] }
                                               ^^
```
Warning: subworkflows/local/target_capture_workflow.nf:94:52: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .combine ( BOWTIE2_ALIGN.out.aligned.map { it = it[1] } )
                                                   ^^
```
Warning: subworkflows/local/target_capture_workflow.nf:94:57: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .combine ( BOWTIE2_ALIGN.out.aligned.map { it = it[1] } )
                                                        ^^
```
Warning: subworkflows/local/target_capture_workflow.nf:95:49: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .combine ( SAMTOOLS_INDEX.out.bai.map { it = it[1] } )
                                                ^^
```
Warning: subworkflows/local/target_capture_workflow.nf:95:54: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .combine ( SAMTOOLS_INDEX.out.bai.map { it = it[1] } )
                                                     ^^
```
Warning: subworkflows/local/target_capture_workflow.nf:104:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_reads = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf:38:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_readsimulator_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_readsimulator_pipeline/main.nf:83:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_readsimulator_pipeline/main.nf:87:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            validateInputSamplesheet(it)
                                     ^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:121:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { processVersionsFromYAML(it) }
                                               ^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:123:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
                .mix(Channel.of(workflowVersionToYAML()))
                     ^^^^^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:264:14: Parameter was not used -- prefix with _ to suppress warning
```
    } catch (all) {
             ^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:350:18: Parameter was not used -- prefix with _ to suppress warning
```
        } catch (all) {
                 ^^^
```
Warning: workflows/readsimulator/main.nf:35:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions        = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/readsimulator/main.nf:36:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files   = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/readsimulator/main.nf:37:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_simulated_reads = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/readsimulator/main.nf:38:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_taxids          = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/readsimulator/main.nf:39:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_accessions      = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/readsimulator/main.nf:40:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta           = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/readsimulator/main.nf:43:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.fromPath(params.fasta)
                   ^^^^^^^
```

Warning: workflows/readsimulator/main.nf:46:29: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_accessions = Channel.fromPath(params.ncbidownload_accessions)
                            ^^^^^^^

Warning: workflows/readsimulator/main.nf:48:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_taxids = Channel.fromPath(params.ncbidownload_taxids)
                        ^^^^^^^
```
Warning: workflows/readsimulator/main.nf:70:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, fasta ->
                ^^^^
```
Warning: workflows/readsimulator/main.nf:76:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_probes = Channel.fromPath(params.probe_file)
                    ^^^^^^^
```
Warning: workflows/readsimulator/main.nf:78:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_probes = Channel.empty()
                    ^^^^^^^
```

Warning: workflows/readsimulator/main.nf:156:23: Parameter was not used -- prefix with _ to suppress warning

            datatype, old_meta, samplesheet ->
                      ^^^^^^^^

Warning: workflows/readsimulator/main.nf:173:68: 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/readsimulator/main.nf:186:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/readsimulator/main.nf:187:69: 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, checkIfExists: true) : Channel.empty()
                                                                    ^^^^^^^

Warning: workflows/readsimulator/main.nf:187:132: 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, checkIfExists: true) : Channel.empty()
                                                                                                                                   ^^^^^^^

Warning: workflows/readsimulator/main.nf:188:67: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                                  ^^^^^^^

Warning: workflows/readsimulator/main.nf:188:128: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                                                                                               ^^^^^^^

Warning: workflows/readsimulator/main.nf:190:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/readsimulator/main.nf:192:45: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
                                            ^^^^^^^

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