Nextflow lint results

Generated: 2026-01-16T10:24:50.067675652Z
Nextflow version: 25.12.0-edge
Summary: 34 errors, 162 warnings

❌ Errors

Error: conf/modules.config:217:17: Unexpected input: ':'

        withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS:UMITOOLS_DEDUP' {
                ^

Error: modules/local/pints/visualizer/main.nf:47:23: chr_name is not defined

    touch ${prefix}_${chr_name}_plus.bigwig
                      ^^^^^^^^

Error: modules/local/pints/visualizer/main.nf:48:23: chr_name is not defined

    touch ${prefix}_${chr_name}_minus.bigwig
                      ^^^^^^^^

Error: modules/nf-core/bwa/index/main.nf:16:27: bwa is not defined

    tuple val(meta), path(bwa) , emit: index
                          ^^^

Error: modules/nf-core/star/align/main.nf:43:20: Unexpected input: ','
```
    def reads1 = [], reads2 = []
                   ^
```

Error: nextflow.config:318:31: manifest is not defined

\033[0;35m  nf-core/nascent ${manifest.version}\033[0m
                              ^^^^^^^^

Error: nextflow.config:321:26: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                         ^^^^^^^^

Error: nextflow.config:321:69: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                    ^^^^^^^^

Error: nextflow.config:321:186: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                                                                         ^^^^^^^^

Error: nextflow.config:330:22: validation is not defined

        beforeText = validation.help.beforeText
                     ^^^^^^^^^^

Error: nextflow.config:331:21: validation is not defined

        afterText = validation.help.afterText
                    ^^^^^^^^^^

Error: subworkflows/local/dreg_prep/main.nf:1:1: Invalid include source: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/nascent/subworkflows/local/modules/nf-core/bedtools/bamtobed/main.nf'
```
include { BEDTOOLS_BAMTOBED } from '../modules/nf-core/bedtools/bamtobed/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/dreg_prep/main.nf:10:5: BEDTOOLS_BAMTOBED is not defined
```
    BEDTOOLS_BAMTOBED(
    ^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/grohmm/main.nf:41:9: Variables in a closure should be declared with def

        filename = "${meta.id}.${meta.single_end ? 'SE': 'PE' }.tuning.csv"
        ^^^^^^^^

Error: subworkflows/local/grohmm/main.nf:45:13: Variables in a closure should be declared with def
```
            meta = [
            ^^^^
```

Error: subworkflows/local/prepare_genome.nf:145:30: UNTAR_DRAGMAP_INDEX is not defined

                ch_dragmap = UNTAR_DRAGMAP_INDEX(dragmap).untar
                             ^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/prepare_genome.nf:146:47: UNTAR_DRAGMAP_INDEX is not defined

                ch_versions = ch_versions.mix(UNTAR_DRAGMAP_INDEX.out.versions)
                                              ^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/prepare_genome.nf:161:36: UNTAR_BOWTIE2_INDEX is not defined

                ch_bowtie2_index = UNTAR_BOWTIE2_INDEX(bowtie2_index).untar
                                   ^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/prepare_genome.nf:162:47: UNTAR_BOWTIE2_INDEX is not defined

                ch_versions = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
                                              ^^^^^^^^^^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:1:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/nascent/modules/nf-core/star/align/main.nf'

include { STAR_ALIGN                                                       } from '../../../modules/nf-core/star/align/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:25:5: STAR_ALIGN is not defined

    STAR_ALIGN ( ch_reads, ch_index, ch_gtf, val_star_ignore_sjdbgtf, val_seq_platform, val_seq_center )
    ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:26:35: STAR_ALIGN is not defined

    ch_versions = ch_versions.mix(STAR_ALIGN.out.versions.first())
                                  ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:31:38: STAR_ALIGN is not defined

    BAM_SORT_STATS_SAMTOOLS_GENOME ( STAR_ALIGN.out.bam, ch_fasta )
                                     ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:41:45: STAR_ALIGN is not defined

    BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME ( STAR_ALIGN.out.bam_transcript, ch_transcripts_fasta )
                                            ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:46:27: STAR_ALIGN is not defined

    orig_bam            = STAR_ALIGN.out.bam                                 // channel: [ val(meta), path(bam)            ]
                          ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:47:27: STAR_ALIGN is not defined

    log_final           = STAR_ALIGN.out.log_final                           // channel: [ val(meta), path(log_final)      ]
                          ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:48:27: STAR_ALIGN is not defined

    log_out             = STAR_ALIGN.out.log_out                             // channel: [ val(meta), path(log_out)        ]
                          ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:49:27: STAR_ALIGN is not defined

    log_progress        = STAR_ALIGN.out.log_progress                        // channel: [ val(meta), path(log_progress)   ]
                          ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:50:27: STAR_ALIGN is not defined

    bam_sorted          = STAR_ALIGN.out.bam_sorted                          // channel: [ val(meta), path(bam)            ]
                          ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:51:27: STAR_ALIGN is not defined

    fastq               = STAR_ALIGN.out.fastq                               // channel: [ val(meta), path(fastq)          ]
                          ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:52:27: STAR_ALIGN is not defined

    tab                 = STAR_ALIGN.out.tab                                 // channel: [ val(meta), path(tab)            ]
                          ^^^^^^^^^^

Error: subworkflows/nf-core/fastq_align_star/main.nf:53:27: STAR_ALIGN is not defined

    orig_bam_transcript = STAR_ALIGN.out.bam_transcript                      // channel: [ val(meta), path(bam)            ]
                          ^^^^^^^^^^

Error: tests/config/test_data.config:6:5: Unexpected input: 'includeConfig'

    includeConfig "https://raw.githubusercontent.com/nf-core/modules/master/tests/config/test_data.config"
    ^

Error: workflows/nascent.nf:278:13: Variables in a closure should be declared with def

            fmeta = meta.findAll { it.key != 'read_group' }
            ^^^^^

⚠️ Warnings

Warning: modules/nf-core/bowtie2/align/main.nf:93:9: Variable was declared but not used

    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
        ^^^^^^^^^

Warning: modules/nf-core/bwa/mem/main.nf:56:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/bwa/mem/main.nf:59:9: Variable was declared but not used

    def samtools_command = sort_bam ? 'sort' : 'view'
        ^^^^^^^^^^^^^^^^

Warning: modules/nf-core/bwamem2/mem/main.nf:59:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/bwamem2/mem/main.nf:62:9: Variable was declared but not used

    def samtools_command = sort_bam ? 'sort' : 'view'
        ^^^^^^^^^^^^^^^^

Warning: modules/nf-core/bwamem2/mem/main.nf:66:9: Variable was declared but not used

    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
        ^^^^^^^^^

Warning: modules/nf-core/cat/cat/main.nf:23:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list = files_in.collect { it.toString() }
                                       ^^
```
Warning: modules/nf-core/cat/cat/main.nf:58:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list   = files_in.collect { it.toString() }
                                         ^^
```
Warning: modules/nf-core/cat/fastq/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/cat/fastq/main.nf:23:59: 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:54:59: 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/custom/getchromsizes/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/deeptools/bamcoverage/main.nf:69:9: Variable was declared but not used

    def extension = args.contains("--outFileFormat bedgraph") || args.contains("-of bedgraph") ? ".bedgraph" : ".bigWig"
        ^^^^^^^^^

Warning: modules/nf-core/dragmap/align/main.nf:58:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/dragmap/align/main.nf:61:9: Variable was declared but not used

    def reads_command = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
        ^^^^^^^^^^^^^

Warning: modules/nf-core/dragmap/align/main.nf:62:9: Variable was declared but not used

    def samtools_command = sort_bam ? 'sort' : 'view'
        ^^^^^^^^^^^^^^^^

Warning: modules/nf-core/dragmap/align/main.nf:66:9: Variable was declared but not used

    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
        ^^^^^^^^^

Warning: modules/nf-core/gffread/main.nf:26:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def extension   = args.contains("-T")       ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' )
                                                                                                      ^^

Warning: modules/nf-core/gffread/main.nf:30:61: Parameter was not used -- prefix with _ to suppress warning

    def args_sorted = args.replaceAll(/(.*)(-[wxy])(.*)/) { all, pre, param, post -> "$pre $post $param" }.trim()
                                                            ^^^

Warning: modules/nf-core/gffread/main.nf:49:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def extension   = args.contains("-T")       ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' )
                                                                                                      ^^

Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/homer/pos2bed/main.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/rseqc/readdistribution/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/rseqc/tin/main.nf:24:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/rseqc/tin/main.nf:38:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/unzip/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: nextflow.config:321:129: Implicit closure parameter is deprecated, declare an explicit parameter instead

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                ^^

Warning: subworkflows/local/align_bwamem2/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/align_dragmap/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/coverage_graphs/main.nf:13:5: Parameter was not used -- prefix with _ to suppress warning
```
    sizes
    ^^^^^
```
Warning: subworkflows/local/coverage_graphs/main.nf:19:5: Variable was declared but not used
```
    bam = bam_bai.map { [it[0], it[1]] }
    ^^^
```
Warning: subworkflows/local/coverage_graphs/main.nf:19:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    bam = bam_bai.map { [it[0], it[1]] }
                         ^^
```
Warning: subworkflows/local/coverage_graphs/main.nf:19:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    bam = bam_bai.map { [it[0], it[1]] }
                                ^^
```
Warning: subworkflows/local/coverage_graphs/main.nf:21:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/dreg_prep/main.nf:6:5: Parameter was not used -- prefix with _ to suppress warning
```
    bai
    ^^^
```
Warning: subworkflows/local/dreg_prep/main.nf:7:5: Parameter was not used -- prefix with _ to suppress warning
```
    sizes
    ^^^^^
```
Warning: subworkflows/local/grohmm/main.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    hisat2_index
    ^^^^^^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:39:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:45:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_fasta = GUNZIP_FASTA([[:], fasta]).gunzip.map { it[1] }
                                                           ^^

Warning: subworkflows/local/prepare_genome.nf:49:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.value(file(fasta))
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:58:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_gtf = GUNZIP_GTF([[:], gtf]).gunzip.map { it[1] }
                                                             ^^

Warning: subworkflows/local/prepare_genome.nf:62:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_gtf = Channel.value(file(gtf))
                         ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:73:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_gtf = GFFREAD(ch_gff, ch_fasta).gtf.map { it[1] }
                                                         ^^

Warning: subworkflows/local/prepare_genome.nf:83:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_gene_bed = GUNZIP_GENE_BED([[:], gene_bed]).gunzip.map { it[1] }
                                                                        ^^

Warning: subworkflows/local/prepare_genome.nf:98:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    CUSTOM_GETCHROMSIZES(ch_fasta.map { [[:], it] })
                                              ^^
```
Warning: subworkflows/local/prepare_genome.nf:99:49: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] }
                                                ^^
```

Warning: subworkflows/local/prepare_genome.nf:100:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] }
                                                          ^^

Warning: subworkflows/local/prepare_genome.nf:106:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bwa_index = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:107:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_dragmap = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:108:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_index = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:122:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_bwa_index = BWA_INDEX(ch_fasta.map { [[:], it] }).index
                                                          ^^

Warning: subworkflows/local/prepare_genome.nf:138:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_bwa_index = BWAMEM2_INDEX(ch_fasta.map { [[:], it] }).index
                                                              ^^

Warning: subworkflows/local/prepare_genome.nf:154:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_dragmap = DRAGMAP_HASHTABLE(ch_fasta.map { [[:], it] }).hashmap
                                                                ^^

Warning: subworkflows/local/prepare_genome.nf:170:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_bowtie2_index = BOWTIE2_BUILD(ch_fasta.map { [[:], it] }).index
                                                                  ^^

Warning: subworkflows/local/quality_control.nf:14:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    bam = bam_bai.map { [it[0], it[1]] }
                         ^^
```
Warning: subworkflows/local/quality_control.nf:14:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    bam = bam_bai.map { [it[0], it[1]] }
                                ^^
```
Warning: subworkflows/local/quality_control.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/transcript_identification/main.nf:25:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/transcript_identification/main.nf:26:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_identification_bed = Channel.empty()
                            ^^^^^^^
```
Warning: subworkflows/local/transcript_identification/main.nf:28:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    grohmm_td_plot = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/transcript_identification/main.nf:37:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    homer_peaks = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/transcript_identification/main.nf:38:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    homer_tagdir = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/transcript_identification/main.nf:54:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { !(it in skip_chr) }
                    ^^
```
Warning: subworkflows/local/transcript_identification/main.nf:96:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_filter_bed = Channel.from(params.filter_bed)
                        ^^^^^^^
```

Warning: subworkflows/local/transcript_identification/main.nf:97:113: Implicit closure parameter is deprecated, declare an explicit parameter instead

        BEDTOOLS_INTERSECT_FILTER(ch_identification_bed.combine(ch_filter_bed.first()), chrom_sizes.map { [[:], it] })
                                                                                                                ^^

Warning: subworkflows/local/transcript_identification/main.nf:102:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_intersect_bed = Channel.from(params.intersect_bed)
                           ^^^^^^^
```

Warning: subworkflows/local/transcript_identification/main.nf:103:109: Implicit closure parameter is deprecated, declare an explicit parameter instead

        BEDTOOLS_INTERSECT(ch_identification_bed.combine(ch_intersect_bed.first()), chrom_sizes.map { [[:], it] })
                                                                                                            ^^

Warning: subworkflows/local/utils_nfcore_nascent_pipeline/main.nf:30:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_nascent_pipeline/main.nf:33:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_nascent_pipeline/main.nf:37:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_nascent_pipeline/main.nf:74:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/nf-core/bam_dedup_stats_samtools_umitools/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_rseqc/main.nf:22:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    bam = bam_bai.map{ [ it[0], it[1] ] }
                         ^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:22:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    bam = bam_bai.map{ [ it[0], it[1] ] }
                                ^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:24:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    versions = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:29:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    bamstat_txt = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:40:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    innerdistance_all      = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:41:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    innerdistance_distance = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:42:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    innerdistance_freq     = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:43:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    innerdistance_mean     = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:44:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    innerdistance_pdf      = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:45:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    innerdistance_rscript  = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:61:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    inferexperiment_txt = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:71:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionannotation_all          = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:72:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionannotation_bed          = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:73:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionannotation_interact_bed = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:74:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionannotation_xls          = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:75:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionannotation_pdf          = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:76:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionannotation_events_pdf   = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:77:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionannotation_rscript      = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:78:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionannotation_log          = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:96:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionsaturation_all     = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:97:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionsaturation_pdf     = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:98:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    junctionsaturation_rscript = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:111:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    readdistribution_txt = Channel.empty()
                           ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:122:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    readduplication_all     = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:123:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    readduplication_seq_xls = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:124:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    readduplication_pos_xls = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:125:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    readduplication_pdf     = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:126:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    readduplication_rscript = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/nf-core/bam_rseqc/main.nf:141:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tin_txt = Channel.empty()
              ^^^^^^^
```
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/fastq_align_bowtie2/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
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/fastq_align_hisat2/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_align_star/main.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/homer_groseq/main.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/homer_groseq/main.nf:22:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_uniqmap = Channel.empty()
                 ^^^^^^^
```

Warning: subworkflows/nf-core/homer_groseq/main.nf:28:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_uniqmap = UNZIP([[:], uniqmap]).unzipped_archive.map { it[1] }
                                                                  ^^

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/nascent.nf:63:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/nascent.nf:64:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/nascent.nf:95:70: 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/nascent.nf:98:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_reads = Channel.empty()
               ^^^^^^^
```
Warning: workflows/nascent.nf:111:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_bam = Channel.empty()
                    ^^^^^^^
```
Warning: workflows/nascent.nf:112:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_bai = Channel.empty()
                    ^^^^^^^
```
Warning: workflows/nascent.nf:113:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_stats = Channel.empty()
                        ^^^^^^^
```
Warning: workflows/nascent.nf:114:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_flagstat = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/nascent.nf:115:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_idxstats = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/nascent.nf:116:5: Variable was declared but not used
```
    ch_star_multiqc = Channel.empty()
    ^^^^^^^^^^^^^^^
```
Warning: workflows/nascent.nf:116:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_star_multiqc = Channel.empty()
                      ^^^^^^^
```

Warning: workflows/nascent.nf:117:5: Variable was declared but not used

    ch_aligner_pca_multiqc = Channel.empty()
    ^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/nascent.nf:117:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_aligner_pca_multiqc = Channel.empty()
                             ^^^^^^^
```

Warning: workflows/nascent.nf:118:5: Variable was declared but not used

    ch_aligner_clustering_multiqc = Channel.empty()
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/nascent.nf:118:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_aligner_clustering_multiqc = Channel.empty()
                                    ^^^^^^^
```
Warning: workflows/nascent.nf:119:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_multiqc = Channel.empty()
                         ^^^^^^^
```

Warning: workflows/nascent.nf:204:9: Variable was declared but not used

        ch_HISAT2_multiqc = FASTQ_ALIGN_HISAT2.out.summary
        ^^^^^^^^^^^^^^^^^

Warning: workflows/nascent.nf:211:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

                PREPARE_GENOME.out.gtf.map { [[:], it] }
                                                   ^^

Warning: workflows/nascent.nf:226:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            PREPARE_GENOME.out.gtf.map { [[:], it] },
                                               ^^
```
Warning: workflows/nascent.nf:231:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.of([[:], []])
            ^^^^^^^
```

Warning: workflows/nascent.nf:235:9: Variable was declared but not used

        ch_transcriptome_bam = FASTQ_ALIGN_STAR.out.bam_transcript
        ^^^^^^^^^^^^^^^^^^^^

Warning: workflows/nascent.nf:237:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.stats.collect { it[1] })
                                                                                     ^^

Warning: workflows/nascent.nf:238:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.flagstat.collect { it[1] })
                                                                                        ^^

Warning: workflows/nascent.nf:239:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.idxstats.collect { it[1] })
                                                                                        ^^

Warning: workflows/nascent.nf:240:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_star_log.collect { it[1] })
                                                                      ^^

Warning: workflows/nascent.nf:278:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            fmeta = meta.findAll { it.key != 'read_group' }
                                   ^^
```
Warning: workflows/nascent.nf:289:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            fmeta = meta.findAll { it.key != 'read_group' }
                                   ^^
```
Warning: workflows/nascent.nf:318:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ).saf.map { it[1] }
                        ^^
```
Warning: workflows/nascent.nf:344:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config = Channel.fromPath(
                        ^^^^^^^
```
Warning: workflows/nascent.nf:349:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.fromPath(params.multiqc_config, checkIfExists: true)
          ^^^^^^^
```
Warning: workflows/nascent.nf:350:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.empty()
          ^^^^^^^
```
Warning: workflows/nascent.nf:352:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ? Channel.fromPath(params.multiqc_logo, checkIfExists: true)
          ^^^^^^^
```
Warning: workflows/nascent.nf:353:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.empty()
          ^^^^^^^
```

Warning: workflows/nascent.nf:359:27: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/nascent.nf:366:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_methods_description = Channel.value(
                             ^^^^^^^
```

Warning: workflows/nascent.nf:378:70: 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/nascent.nf:379:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(ch_bowtie2_multiqc.collect { it[1] }.ifEmpty([]))
                                                                         ^^

Warning: workflows/nascent.nf:380:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_stats.collect { it[1] }.ifEmpty([]))
                                                                        ^^

Warning: workflows/nascent.nf:381:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_flagstat.collect { it[1] }.ifEmpty([]))
                                                                           ^^

Warning: workflows/nascent.nf:382:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_idxstats.collect { it[1] }.ifEmpty([]))
                                                                           ^^

Warning: workflows/nascent.nf:383:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/nascent.nf:384:91: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/nascent.nf:385:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/nascent.nf:386:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/nascent.nf:387:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/nascent.nf:388:95: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/nascent.nf:389:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(ch_grohmm_multiqc.collect { it[1] }.ifEmpty([]))
                                                                        ^^

Warning: workflows/nascent.nf:390:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(ch_homer_multiqc.collect { it[1] }.ifEmpty([]))
                                                                       ^^

Warning: workflows/nascent.nf:391:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/nascent.nf:392:94: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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