Nextflow lint results

Generated: 2026-01-16T10:24:01.003313220Z
Nextflow version: 25.12.0-edge
Summary: 3 errors, 65 warnings

❌ Errors

Error: modules/nf-core/rastair/mbiasparser/main.nf:15:26: trim_OT is not defined

    tuple val(meta), env(trim_OT), env(trim_OB),                    emit: mbias_processed_str
                         ^^^^^^^

Error: modules/nf-core/rastair/mbiasparser/main.nf:15:40: trim_OB is not defined

    tuple val(meta), env(trim_OT), env(trim_OB),                    emit: mbias_processed_str
                                       ^^^^^^^

Error: nextflow.config:251:23: Invalid include source: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/methylseq/conf/aws/batch/nextflow.config'
```
    aws_batch       { includeConfig 'conf/aws/batch/nextflow.config' }
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

⚠️ Warnings

Warning: conf/modules/bismark_genomepreparation.config:9:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            saveAs: { it =~ /.*\.yml/ ? null : it },
                      ^^
```
Warning: conf/modules/bismark_genomepreparation.config:9:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            saveAs: { it =~ /.*\.yml/ ? null : it },
                                               ^^
```
Warning: conf/modules/bwameth_index.config:7:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            saveAs: { it.equals('versions.yml') ? null : it.tokenize("/").last() },
                      ^^
```

Warning: conf/modules/bwameth_index.config:7:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { it.equals('versions.yml') ? null : it.tokenize("/").last() },
                                                         ^^

Warning: modules/nf-core/bismark/align/main.nf:51:18: Parameter was not used -- prefix with _ to suppress warning
```
        } catch (all) {
                 ^^^
```
Warning: modules/nf-core/bismark/align/main.nf:67:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bismark/coverage2cytosine/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bismark/deduplicate/main.nf:23:9: Variable was declared but not used
```
    def prefix  = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/bismark/deduplicate/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bismark/genomepreparation/main.nf:34:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bismark/methylationextractor/main.nf:54:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bismark/report/main.nf:32:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bismark/summary/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bismark/summary/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bwameth/index/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bwameth/index/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/cat/fastq/main.nf:22:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
                                                           ^^

Warning: modules/nf-core/cat/fastq/main.nf:58:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
                                                           ^^

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

Warning: modules/nf-core/parabricks/fq2bammeth/main.nf:35:83: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def known_sites_command = known_sites ? known_sites.collect { "--knownSites ${it}" }.join(' ') : ""
                                                                                  ^^

Warning: modules/nf-core/rastair/call/main.nf:25:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/rastair/mbias/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/trimgalore/main.nf:47:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        args_list.removeAll { it.toLowerCase().contains('_r2 ') }
                              ^^
```
Warning: subworkflows/local/targeted_sequencing/main.nf:28:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/targeted_sequencing/main.nf:29:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_picard_metrics = Channel.empty()
                        ^^^^^^^
```

Warning: subworkflows/local/targeted_sequencing/main.nf:70:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_intervals = PICARD_BEDTOINTERVALLIST.out.intervallist.map { it[1] }
                                                                       ^^

Warning: subworkflows/local/utils_nfcore_methylseq_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_methylseq_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_methylseq_pipeline/main.nf:109:37: Parameter was not used -- prefix with _ to suppress warning

            meta, fastq_1, fastq_2, genome ->
                                    ^^^^^^

Warning: subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf:241:9: Variable was declared but not used
```
    def citation_text = [
        ^^^^^^^^^^^^^
```
Warning: subworkflows/nf-core/bam_methyldackel/main.nf:13:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_methydackel_extract_bedgraph  = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/nf-core/bam_methyldackel/main.nf:14:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_methydackel_extract_methylkit = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/nf-core/bam_methyldackel/main.nf:15:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_methydackel_mbias             = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/nf-core/bam_methyldackel/main.nf:16:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files                 = Channel.empty()
                                       ^^^^^^^
```
Warning: subworkflows/nf-core/bam_methyldackel/main.nf:17:40: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions                      = Channel.empty()
                                       ^^^^^^^
```

Warning: subworkflows/nf-core/bam_methyldackel/main.nf:45:65: Parameter was not used -- prefix with _ to suppress warning

    ch_multiqc_files = ch_methydackel_extract_bedgraph.collect{ meta, bedgraph -> bedgraph  }
                                                                ^^^^

Warning: subworkflows/nf-core/bam_methyldackel/main.nf:46:72: Parameter was not used -- prefix with _ to suppress warning

                        .mix(ch_methydackel_extract_methylkit.collect{ meta, methylkit -> methylkit })
                                                                       ^^^^

Warning: subworkflows/nf-core/bam_methyldackel/main.nf:47:60: Parameter was not used -- prefix with _ to suppress warning

                        .mix(ch_methydackel_mbias.collect{ meta, txt -> txt  })
                                                           ^^^^

Warning: subworkflows/nf-core/bam_sort_stats_samtools/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/bam_stats_samtools/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/bam_taps_conversion/main.nf:21:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_rastair_mbias = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/bam_taps_conversion/main.nf:22:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_rastair_call  = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/bam_taps_conversion/main.nf:23:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions      = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/nf-core/bam_taps_conversion/main.nf:47:53: Parameter was not used -- prefix with _ to suppress warning

        ch_rastair_mbiasparser.map{ meta, nOT_clip, nOB_clip -> [ meta, nOT_clip ] },
                                                    ^^^^^^^^

Warning: subworkflows/nf-core/bam_taps_conversion/main.nf:48:43: Parameter was not used -- prefix with _ to suppress warning

        ch_rastair_mbiasparser.map{ meta, nOT_clip, nOB_clip -> [ meta, nOB_clip ] },
                                          ^^^^^^^^

Warning: subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf:20:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta         = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf:21:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta_index   = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf:22:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bismark_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf:23:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bwameth_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf:24:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions      = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf:29:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            gzipped: it[1].toString().endsWith('.gz')
                     ^^
```
Warning: subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf:50:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    gzipped: it[1].toString().endsWith('.gz')
                             ^^
```
Warning: subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf:79:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    gzipped: it[1].toString().endsWith('.gz')
                             ^^
```
Warning: subworkflows/nf-core/fasta_index_methylseq/main.nf:34:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            gzipped: it[1].toString().endsWith('.gz')
                     ^^
```
Warning: subworkflows/nf-core/fasta_index_methylseq/main.nf:55:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    gzipped: it[1].toString().endsWith('.gz')
                             ^^
```
Warning: subworkflows/nf-core/fasta_index_methylseq/main.nf:93:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    gzipped: it[1].toString().endsWith('.gz')
                             ^^
```
Warning: subworkflows/nf-core/fasta_index_methylseq/main.nf:123:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    gzipped: it[1].toString().endsWith('.gz')
                             ^^
```
Warning: subworkflows/nf-core/fastq_align_bwa/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

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/methylseq/main.nf:198:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_versions    = ch_versions.mix(FASTQ_ALIGN_DEDUP_BWAMEM.out.versions.unique{ it.baseName })
                                                                                       ^^

Warning: workflows/methylseq/main.nf:368:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/methylseq/main.nf:371:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/methylseq/main.nf:375:81: 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/methylseq/main.nf:379:105: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/methylseq/main.nf:383:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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