Nextflow lint results

Generated: 2026-01-16T10:20:41.560150878Z
Nextflow version: 25.12.0-edge
Summary: 75 errors, 53 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( 1                  , 'cpus'    ) }
                   ^^^^^^^^^

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

        memory = { check_max( 6.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( 2     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

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

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

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

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

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

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

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

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

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

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

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

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

Error: conf/base.config:46:20: check_max is not defined

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

Error: conf/base.config:47:20: check_max is not defined

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

Error: conf/base.config:50:20: check_max is not defined

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

Error: conf/base.config:53:20: check_max is not defined

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

Error: main.nf:23:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/local/utils_nfcore_evexplorer_pipeline/main.nf'

include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_evexplorer_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:24:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/local/utils_nfcore_evexplorer_pipeline/main.nf'

include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_evexplorer_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:25:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/local/utils_nfcore_evexplorer_pipeline/main.nf'

include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_evexplorer_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:35:16: getGenomeAttribute is not defined

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

Error: main.nf:41:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_gtf_1     = Channel.fromPath(params.gtf_1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: main.nf:42:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_gtf_2     = Channel.fromPath(params.gtf_2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: main.nf:43:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_chr_names = Channel.fromPath(params.chr_names)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: main.nf:44:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_fasta     = Channel.fromPath(params.fasta, checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:71:9: ch_fasta is not defined
```
        ch_fasta,
        ^^^^^^^^
```
Error: main.nf:72:9: ch_gtf_1 is not defined
```
        ch_gtf_1,
        ^^^^^^^^
```
Error: main.nf:73:9: ch_gtf_2 is not defined
```
        ch_gtf_2,
        ^^^^^^^^
```

Error: main.nf:74:9: ch_chr_names is not defined

        ch_chr_names
        ^^^^^^^^^^^^

Error: main.nf:80:9: ch_fasta is not defined
```
        ch_fasta,
        ^^^^^^^^
```
Error: main.nf:81:9: ch_gtf_1 is not defined
```
        ch_gtf_1,
        ^^^^^^^^
```
Error: main.nf:82:9: ch_gtf_2 is not defined
```
        ch_gtf_2,
        ^^^^^^^^
```

Error: main.nf:83:9: ch_chr_names is not defined

        ch_chr_names
        ^^^^^^^^^^^^

Error: main.nf:107:5: PIPELINE_INITIALISATION is not defined

    PIPELINE_INITIALISATION (
    ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:120:9: PIPELINE_INITIALISATION is not defined

        PIPELINE_INITIALISATION.out.samplesheet,
        ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:123:6: PIPELINE_COMPLETION is not defined

	    PIPELINE_COMPLETION (
     ^^^^^^^^^^^^^^^^^^^

Error: modules/local/derfinder/main.nf:12:15: meta is already declared
```
    tuple val(meta), path(path_bai)
              ^^^^
```

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

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

Error: nextflow.config:67:5: Unexpected input: 'includeConfig'

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

Error: subworkflows/local/utils_nfcore_evexplorer_pipeline/main.nf:248:21: Unexpected input: 'doi_ref'

        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
                    ^

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:73:17: Unexpected input: 'doi_ref'

    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
                ^

Error: workflows/evexplorer.nf:9:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/modules/nf-core/multiqc/main.nf'
```
include { MULTIQC                   } from '../modules/nf-core/multiqc/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/evexplorer.nf:19:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { paramsSummaryMultiqc      } from '../subworkflows/nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/evexplorer.nf:20:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { softwareVersionsToYAML    } from '../subworkflows/nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/evexplorer.nf:21:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/local/utils_nfcore_evexplorer_pipeline/main.nf'
```
include { methodsDescriptionText    } from '../subworkflows/local/utils_nfcore_evexplorer_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/evexplorer.nf:138:18: _ is not allowed as an identifier because it is reserved for future use
```
    .map { meta, _ -> tuple(meta.id, meta.sample_batch) }
                 ^
```
Error: workflows/evexplorer.nf:150:18: _ is not allowed as an identifier because it is reserved for future use
```
    .map { meta, _ -> tuple(meta.id, meta.sample_batch, meta.sample_cond ) }
                 ^
```
Error: workflows/evexplorer.nf:163:5: softwareVersionsToYAML is not defined
```
    softwareVersionsToYAML(ch_versions)
    ^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/evexplorer.nf:186:41: paramsSummaryMultiqc is not defined

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

Error: workflows/evexplorer.nf:193:9: methodsDescriptionText is not defined

        methodsDescriptionText(ch_multiqc_custom_methods_description))
        ^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/evexplorer.nf:203:5: MULTIQC is not defined
```
    MULTIQC (
    ^^^^^^^
```

Error: workflows/evexplorer.nf:212:27: MULTIQC is not defined

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

Error: workflows/long_reads.nf:11:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/modules/nf-core/multiqc/main.nf'
```
include { MULTIQC                   } from '../modules/nf-core/multiqc/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/long_reads.nf:20:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { paramsSummaryMultiqc      } from '../subworkflows/nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/long_reads.nf:21:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { softwareVersionsToYAML    } from '../subworkflows/nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/long_reads.nf:22:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/local/utils_nfcore_evexplorer_pipeline/main.nf'
```
include { methodsDescriptionText    } from '../subworkflows/local/utils_nfcore_evexplorer_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/long_reads.nf:116:18: _ is not allowed as an identifier because it is reserved for future use
```
    .map { meta, _ -> tuple(meta.id, meta.sample_batch) }
                 ^
```
Error: workflows/long_reads.nf:128:18: _ is not allowed as an identifier because it is reserved for future use
```
    .map { meta, _ -> tuple(meta.id, meta.sample_batch, meta.sample_cond ) }
                 ^
```
Error: workflows/long_reads.nf:142:5: softwareVersionsToYAML is not defined
```
    softwareVersionsToYAML(ch_versions)
    ^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/long_reads.nf:165:41: paramsSummaryMultiqc is not defined

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

Error: workflows/long_reads.nf:172:9: methodsDescriptionText is not defined

        methodsDescriptionText(ch_multiqc_custom_methods_description))
        ^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/long_reads.nf:182:5: MULTIQC is not defined
```
    MULTIQC (
    ^^^^^^^
```

Error: workflows/long_reads.nf:191:27: MULTIQC is not defined

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

Error: workflows/small_reads.nf:9:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/modules/nf-core/multiqc/main.nf'
```
include { MULTIQC                   } from '../modules/nf-core/multiqc/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/small_reads.nf:19:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { paramsSummaryMultiqc      } from '../subworkflows/nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/small_reads.nf:20:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { softwareVersionsToYAML    } from '../subworkflows/nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/small_reads.nf:21:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/evexplorer/subworkflows/local/utils_nfcore_evexplorer_pipeline/main.nf'
```
include { methodsDescriptionText    } from '../subworkflows/local/utils_nfcore_evexplorer_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/small_reads.nf:138:18: _ is not allowed as an identifier because it is reserved for future use
```
    .map { meta, _ -> tuple(meta.id, meta.sample_batch) }
                 ^
```
Error: workflows/small_reads.nf:150:18: _ is not allowed as an identifier because it is reserved for future use
```
    .map { meta, _ -> tuple(meta.id, meta.sample_batch, meta.sample_cond ) }
                 ^
```
Error: workflows/small_reads.nf:163:5: softwareVersionsToYAML is not defined
```
    softwareVersionsToYAML(ch_versions)
    ^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/small_reads.nf:186:41: paramsSummaryMultiqc is not defined

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

Error: workflows/small_reads.nf:193:9: methodsDescriptionText is not defined

        methodsDescriptionText(ch_multiqc_custom_methods_description))
        ^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/small_reads.nf:203:5: MULTIQC is not defined
```
    MULTIQC (
    ^^^^^^^
```

Error: workflows/small_reads.nf:212:27: MULTIQC is not defined

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

⚠️ Warnings

Warning: main.nf:41:1: Variable was declared but not used

ch_gtf_1     = Channel.fromPath(params.gtf_1)
^^^^^^^^

Warning: main.nf:41:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_gtf_1     = Channel.fromPath(params.gtf_1)
               ^^^^^^^
```

Warning: main.nf:42:1: Variable was declared but not used

ch_gtf_2     = Channel.fromPath(params.gtf_2)
^^^^^^^^

Warning: main.nf:42:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_gtf_2     = Channel.fromPath(params.gtf_2)
               ^^^^^^^
```

Warning: main.nf:43:1: Variable was declared but not used

ch_chr_names = Channel.fromPath(params.chr_names)
^^^^^^^^^^^^

Warning: main.nf:43:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_chr_names = Channel.fromPath(params.chr_names)
               ^^^^^^^
```

Warning: main.nf:44:1: Variable was declared but not used

ch_fasta     = Channel.fromPath(params.fasta, checkIfExists: true)
^^^^^^^^

Warning: main.nf:44:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_fasta     = Channel.fromPath(params.fasta, checkIfExists: true)
               ^^^^^^^
```
Warning: modules/local/derfinder/main.nf:11:15: Variable was declared but not used
```
    tuple val(meta), path(path_bam)
              ^^^^
```

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/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

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/pychopper/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/star/align/main.nf:46:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

    meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
                                                       ^^

Warning: workflows/evexplorer.nf:40:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/evexplorer.nf:41:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/evexplorer.nf:63:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/evexplorer.nf:81:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/evexplorer.nf:118:12: Parameter was not used -- prefix with _ to suppress warning
```
    .map { meta, bam -> tuple([id: 'sample1', single_end: true], bam) }
           ^^^^
```

Warning: workflows/evexplorer.nf:122:12: Parameter was not used -- prefix with _ to suppress warning

    .map { meta, index -> tuple([id: 'sample1', single_end: true], index) }
           ^^^^

Warning: workflows/evexplorer.nf:175:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/evexplorer.nf:178:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/evexplorer.nf:179:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/evexplorer.nf:181:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/evexplorer.nf:182:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/evexplorer.nf:186:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

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

    ch_methods_description                = Channel.value(
                                            ^^^^^^^

Warning: workflows/long_reads.nf:41:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/long_reads.nf:42:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/long_reads.nf:61:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/long_reads.nf:79:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/long_reads.nf:98:12: Parameter was not used -- prefix with _ to suppress warning

    .map { meta, bam -> tuple([id: 'sample1', single_end: true], bam) }
           ^^^^

Warning: workflows/long_reads.nf:102:12: Parameter was not used -- prefix with _ to suppress warning

    .map { meta, index -> tuple([id: 'sample1', single_end: true], index) }
           ^^^^

Warning: workflows/long_reads.nf:154:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/long_reads.nf:157:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/long_reads.nf:158:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/long_reads.nf:160:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/long_reads.nf:161:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/long_reads.nf:165:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

Warning: workflows/long_reads.nf:171:45: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_methods_description                = Channel.value(
                                            ^^^^^^^

Warning: workflows/small_reads.nf:40:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/small_reads.nf:41:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/small_reads.nf:63:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/small_reads.nf:81:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/small_reads.nf:118:12: Parameter was not used -- prefix with _ to suppress warning
```
    .map { meta, bam -> tuple([id: 'sample1', single_end: true], bam) }
           ^^^^
```

Warning: workflows/small_reads.nf:122:12: Parameter was not used -- prefix with _ to suppress warning

    .map { meta, index -> tuple([id: 'sample1', single_end: true], index) }
           ^^^^

Warning: workflows/small_reads.nf:175:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/small_reads.nf:178:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/small_reads.nf:179:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/small_reads.nf:181:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/small_reads.nf:182:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/small_reads.nf:186:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

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

    ch_methods_description                = Channel.value(
                                            ^^^^^^^

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