Nextflow lint results

Generated: 2026-01-16T10:28:30.475825624Z
Nextflow version: 25.12.0-edge
Summary: 49 errors, 190 warnings

❌ Errors

Error: conf/modules.config:915:13: Unexpected input: ':'
```
    withName: 'MULTIQC' {
            ^
```
Error: main.nf:41:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/rnasplice/workflows/rnasplice.nf'
```
include { RNASPLICE } from './workflows/rnasplice'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: main.nf:67:5: RNASPLICE is not defined
```
    RNASPLICE ()
    ^^^^^^^^^
```

Error: main.nf:79:9: RNASPLICE is not defined

        RNASPLICE.out.final_multiqc_report
        ^^^^^^^^^

Error: modules/local/create_bamlist_single.nf:13:34: cond is not defined

    tuple val(contrast), path("${cond}_bamlist.txt"), emit: bamlist
                                 ^^^^

Error: modules/local/create_bamlist_single.nf:21:10: bam is not defined

    echo $bam | sed 's: :,:g' > ${cond}_bamlist.txt
         ^^^^

Error: modules/local/create_bamlist_single.nf:21:35: cond is not defined

    echo $bam | sed 's: :,:g' > ${cond}_bamlist.txt
                                  ^^^^

Error: modules/local/dexseq_annotation.nf:26:9: aggregation is already declared

    def aggregation = aggregation ? '' : '-r no'
        ^^^^^^^^^^^

Error: modules/local/dexseq_count.nf:28:9: alignment_quality is already declared

    def alignment_quality = "-a ${alignment_quality}"
        ^^^^^^^^^^^^^^^^^

Error: modules/local/rmats_prep_single.nf:60:14: bam_group1 is not defined
```
        --b1 $bam_group1 \\
             ^^^^^^^^^^^
```
Error: modules/local/samplesheet_check.nf:24:22: Unexpected input: '\n'
```
        case 'fastq':
                     ^
```

Error: modules/local/star_align_igenomes.nf:40:9: seq_platform is already declared

    def seq_platform    = seq_platform ? "'PL:$seq_platform'" : ""
        ^^^^^^^^^^^^

Error: modules/local/star_align_igenomes.nf:41:9: seq_center is already declared

    def seq_center      = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
        ^^^^^^^^^^

Error: modules/local/suppa_clusterevents.nf:4:5: Invalid process directive
```
    stageInMode = 'copy'
    ^^^^^^^^^^^^^^^^^^^^
```
Error: modules/local/suppa_clusterevents.nf:13:15: cond1 is already declared
```
    tuple val(cond1), val(cond2), path(psivec)
              ^^^^^
```

Error: modules/local/suppa_clusterevents.nf:13:27: cond2 is already declared

    tuple val(cond1), val(cond2), path(psivec)
                          ^^^^^

Error: modules/local/suppa_clusterevents.nf:14:15: cond1 is already declared

    tuple val(cond1), val(cond2), val(group_ranges) // e.g. 1-3,4-6
              ^^^^^

Error: modules/local/suppa_clusterevents.nf:14:27: cond2 is already declared

    tuple val(cond1), val(cond2), val(group_ranges) // e.g. 1-3,4-6
                          ^^^^^

Error: modules/local/suppa_clusterevents.nf:34:9: clusterevents_sigthreshold is already declared

    def clusterevents_sigthreshold  = clusterevents_sigthreshold ? "-st ${params.clusterevents_sigthreshold}" : ''
        ^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/suppa_clusterevents.nf:35:9: clusterevents_separation is already declared

    def clusterevents_separation = clusterevents_separation ? "-s ${params.clusterevents_separation}" : ''
        ^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/suppa_diffsplice.nf:13:15: cond1 is already declared

    tuple val(cond1), val(cond2), path(psi1), path(psi2)
              ^^^^^

Error: modules/local/suppa_diffsplice.nf:13:27: cond2 is already declared

    tuple val(cond1), val(cond2), path(psi1), path(psi2)
                          ^^^^^

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

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

Error: modules/nf-core/star/align/main.nf:43:20: Unexpected input: ','
```
    def reads1 = [], reads2 = []
                   ^
```
Error: nextflow.config:302:5: Unexpected input: 'includeConfig'
```
    includeConfig 'conf/igenomes.config'
    ^
```
Error: subworkflows/local/align_star.nf:5:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/rnasplice/modules/nf-core/star/align/main.nf'
```
include { STAR_ALIGN               } from '../../modules/nf-core/star/align/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/align_star.nf:51:9: STAR_ALIGN is not defined

        STAR_ALIGN ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
        ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:52:29: STAR_ALIGN is not defined

        ch_orig_bam       = STAR_ALIGN.out.bam
                            ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:53:29: STAR_ALIGN is not defined

        ch_log_final      = STAR_ALIGN.out.log_final
                            ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:54:29: STAR_ALIGN is not defined

        ch_log_out        = STAR_ALIGN.out.log_out
                            ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:55:29: STAR_ALIGN is not defined

        ch_log_progress   = STAR_ALIGN.out.log_progress
                            ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:56:29: STAR_ALIGN is not defined

        ch_bam_sorted     = STAR_ALIGN.out.bam_sorted
                            ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:57:29: STAR_ALIGN is not defined

        ch_bam_transcript = STAR_ALIGN.out.bam_transcript
                            ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:58:29: STAR_ALIGN is not defined

        ch_fastq          = STAR_ALIGN.out.fastq
                            ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:59:29: STAR_ALIGN is not defined

        ch_tab            = STAR_ALIGN.out.tab
                            ^^^^^^^^^^

Error: subworkflows/local/align_star.nf:60:45: STAR_ALIGN is not defined

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

Error: subworkflows/local/input_check.nf:15:22: Unexpected input: '\n'
```
        case 'fastq':
                     ^
```

Error: subworkflows/local/tx2gene_tximport.nf:27:13: Variables in a closure should be declared with def

            tgz = prefix[0].toString().endsWith(".tar.gz") ? true : false
            ^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:59:31: reads is already declared

                        meta, reads ->
                              ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:88:23: reads is already declared

                meta, reads, trim_log ->
                      ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:88:30: trim_log is already declared

                meta, reads, trim_log ->
                             ^^^^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:90:25: Variables in a closure should be declared with def

                        num_reads = getTrimGaloreReadsAfterFiltering(meta.single_end ? trim_log : trim_log[-1])
                        ^^^^^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:99:29: reads is already declared

            .filter { meta, reads, num_reads -> num_reads >= min_trimmed_reads.toFloat() }
                            ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:99:36: num_reads is already declared

            .filter { meta, reads, num_reads -> num_reads >= min_trimmed_reads.toFloat() }
                                   ^^^^^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:100:26: reads is already declared

            .map { meta, reads, num_reads -> [ meta, reads ] }
                         ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:100:33: num_reads is already declared

            .map { meta, reads, num_reads -> [ meta, reads ] }
                                ^^^^^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:104:26: reads is already declared

            .map { meta, reads, num_reads -> [ meta, num_reads ] }
                         ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:104:33: num_reads is already declared

            .map { meta, reads, num_reads -> [ meta, num_reads ] }
                                ^^^^^^^^^

Error: workflows/rnasplice.nf:155:22: Unexpected input: '\n'
```
        case 'fastq':
                     ^
```

⚠️ Warnings

Warning: modules/local/dexseq_annotation.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/dexseq_count.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/drimseq_filter.nf:30:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/isoformswitchanalyzer.nf:29:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/rmats_post.nf:33:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/rmats_post_single.nf:32:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/rmats_prep.nf:31:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/rmats_prep_single.nf:31:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/stager.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/suppa_clusterevents.nf:12:15: Variable was declared but not used
```
    tuple val(cond1), val(cond2), path(dpsi)
              ^^^^^
```
Warning: modules/local/suppa_clusterevents.nf:12:27: Variable was declared but not used
```
    tuple val(cond1), val(cond2), path(dpsi)
                          ^^^^^
```
Warning: modules/local/suppa_clusterevents.nf:13:15: Variable was declared but not used
```
    tuple val(cond1), val(cond2), path(psivec)
              ^^^^^
```
Warning: modules/local/suppa_clusterevents.nf:13:27: Variable was declared but not used
```
    tuple val(cond1), val(cond2), path(psivec)
                          ^^^^^
```
Warning: modules/local/suppa_diffsplice.nf:12:15: Variable was declared but not used
```
    tuple val(cond1), val(cond2), path(tpm1), path(tpm2)
              ^^^^^
```

Warning: modules/local/suppa_diffsplice.nf:12:27: Variable was declared but not used

    tuple val(cond1), val(cond2), path(tpm1), path(tpm2)
                          ^^^^^

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/dumpsoftwareversions/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
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/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/rsem/preparereference/main.nf:27:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        args_list.removeIf { it.contains('--star') }
                             ^^
```
Warning: modules/nf-core/samtools/flagstat/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/samtools/idxstats/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/samtools/stats/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/trimgalore/main.nf:41:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        args_list.removeAll { it.toLowerCase().contains('_r2 ') }
                              ^^
```
Warning: modules/nf-core/ucsc/bedclip/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ucsc/bedgraphtobigwig/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/align_star.nf:24:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/align_star.nf:30:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_orig_bam       = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/align_star.nf:31:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_log_final      = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/align_star.nf:32:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_log_out        = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/align_star.nf:33:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_log_progress   = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/align_star.nf:34:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bam_sorted     = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/align_star.nf:35:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bam_transcript = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/align_star.nf:36:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fastq          = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/align_star.nf:37:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_tab            = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/dexseq_deu.nf:24:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/dexseq_deu.nf:61:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        DEXSEQ_COUNT.out.dexseq_clean_txt.map{ it[1] }.collect(),
                                               ^^
```

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

    dexseq_clean_txt        = DEXSEQ_COUNT.out.dexseq_clean_txt.map{ it[1] }.collect()
                                                                     ^^

Warning: subworkflows/local/drimseq_dexseq_dtu.nf:27:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/edger_deu.nf:21:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/edger_deu.nf:42:51: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        SUBREAD_FEATURECOUNTS.out.counts.collect({it[1]}),
                                                  ^^
```
Warning: subworkflows/local/leafcutter.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/leafcutter.nf:18:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { it[1] }
               ^^
```
Warning: subworkflows/local/prepare_genome.nf:43:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:49:68: 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:52:20: 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:60:68: 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:63:22: 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:67:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_gff      = GUNZIP_GFF ( [ [:], gff ] ).gunzip.map { it[1] }
                                                                   ^^

Warning: subworkflows/local/prepare_genome.nf:70:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_gff = Channel.value(file(gff))
                     ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:82:102: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_transcript_fasta = GUNZIP_TRANSCRIPT_FASTA ( [ [:], transcript_fasta ] ).gunzip.map { it[1] }
                                                                                                     ^^

Warning: subworkflows/local/prepare_genome.nf:85:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_transcript_fasta = Channel.value(file(transcript_fasta))
                                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:102:50: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    CUSTOM_GETCHROMSIZES ( ch_fasta.map { [ [:], it ] } )
                                                 ^^
```

Warning: subworkflows/local/prepare_genome.nf:103:57: 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:104:59: 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:110:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_star_index = Channel.empty()
                    ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:114:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map { it[1] }
                                                                                     ^^

Warning: subworkflows/local/prepare_genome.nf:117:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_star_index = Channel.value(file(star_index))
                                ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:133:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_salmon_index = Channel.empty()
                      ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:137:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_salmon_index = UNTAR_SALMON_INDEX ( [ [:], salmon_index ] ).untar.map { it[1] }
                                                                                           ^^

Warning: subworkflows/local/prepare_genome.nf:140:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_salmon_index = Channel.value(file(salmon_index))
                                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:153:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_dexseq_gff = Channel.empty()
                    ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:156:84: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_dexseq_gff = GUNZIP_GFF_DEXSEQ ( [ [:], gff_dexseq ] ).gunzip.map { it[1] }
                                                                                   ^^

Warning: subworkflows/local/prepare_genome.nf:159:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_dexseq_gff = Channel.value(file(gff_dexseq))
                            ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:166:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_suppa_tpm = Channel.empty()
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:169:81: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_suppa_tpm = GUNZIP_SUPPA_TPM ( [ [:], suppa_tpm ] ).gunzip.map { it[1] }
                                                                                ^^

Warning: subworkflows/local/prepare_genome.nf:172:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_suppa_tpm = Channel.value(file(suppa_tpm))
                           ^^^^^^^
```
Warning: subworkflows/local/rmats.nf:29:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/rmats.nf:57:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bam = ch_contrasts.map { [ it.contrast, it.treatment, it.bam1 ] }
                                      ^^

Warning: subworkflows/local/rmats.nf:57:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bam = ch_contrasts.map { [ it.contrast, it.treatment, it.bam1 ] }
                                                   ^^

Warning: subworkflows/local/rmats.nf:57:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bam = ch_contrasts.map { [ it.contrast, it.treatment, it.bam1 ] }
                                                                 ^^

Warning: subworkflows/local/rmats.nf:82:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text ] }
                                                    ^^

Warning: subworkflows/local/rmats.nf:82:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text ] }
                                                                 ^^

Warning: subworkflows/local/rmats.nf:82:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text ] }
                                                                               ^^

Warning: subworkflows/local/rmats.nf:82:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text ] }
                                                                                         ^^

Warning: subworkflows/local/rmats.nf:82:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text ] }
                                                                                                  ^^

Warning: subworkflows/local/rmats.nf:113:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text, it.rmats_temp ] }
                                                    ^^

Warning: subworkflows/local/rmats.nf:113:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text, it.rmats_temp ] }
                                                                 ^^

Warning: subworkflows/local/rmats.nf:113:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text, it.rmats_temp ] }
                                                                               ^^

Warning: subworkflows/local/rmats.nf:113:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text, it.rmats_temp ] }
                                                                                         ^^

Warning: subworkflows/local/rmats.nf:113:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text, it.rmats_temp ] }
                                                                                                  ^^

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

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.meta1, it.bam1, it.bam1_text, it.rmats_temp ] }
                                                                                                                ^^

Warning: subworkflows/local/rmats.nf:143:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bam = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.bam1, it.bam2 ] }
                                      ^^

Warning: subworkflows/local/rmats.nf:143:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bam = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.bam1, it.bam2 ] }
                                                   ^^

Warning: subworkflows/local/rmats.nf:143:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bam = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.bam1, it.bam2 ] }
                                                                 ^^

Warning: subworkflows/local/rmats.nf:143:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bam = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.bam1, it.bam2 ] }
                                                                             ^^

Warning: subworkflows/local/rmats.nf:143:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bam = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.bam1, it.bam2 ] }
                                                                                      ^^

Warning: subworkflows/local/rmats.nf:168:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                    ^^

Warning: subworkflows/local/rmats.nf:168:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                                 ^^

Warning: subworkflows/local/rmats.nf:168:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                                               ^^

Warning: subworkflows/local/rmats.nf:168:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                                                           ^^

Warning: subworkflows/local/rmats.nf:168:102: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                                                                     ^^

Warning: subworkflows/local/rmats.nf:168:112: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                                                                               ^^

Warning: subworkflows/local/rmats.nf:168:121: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                                                                                        ^^

Warning: subworkflows/local/rmats.nf:168:130: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                                                                                                 ^^

Warning: subworkflows/local/rmats.nf:168:144: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text ] }
                                                                                                                                               ^^

Warning: subworkflows/local/rmats.nf:199:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                    ^^

Warning: subworkflows/local/rmats.nf:199:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                 ^^

Warning: subworkflows/local/rmats.nf:199:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                               ^^

Warning: subworkflows/local/rmats.nf:199:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                                           ^^

Warning: subworkflows/local/rmats.nf:199:102: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                                                     ^^

Warning: subworkflows/local/rmats.nf:199:112: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                                                               ^^

Warning: subworkflows/local/rmats.nf:199:121: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                                                                        ^^

Warning: subworkflows/local/rmats.nf:199:130: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                                                                                 ^^

Warning: subworkflows/local/rmats.nf:199:144: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                                                                                               ^^

Warning: subworkflows/local/rmats.nf:199:158: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_contrasts_bamlist = ch_contrasts.map { [ it.contrast, it.treatment, it.control, it.meta1, it.meta2, it.bam1, it.bam2, it.bam1_text, it.bam2_text, it.rmats_temp ] }
                                                                                                                                                             ^^

Warning: subworkflows/local/suppa.nf:63:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:84:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_ioe_events             = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:85:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_suppa_local_psi        = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:86:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_split_suppa_local_psi  = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:88:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_dpsi_local             = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:89:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_psivec_local           = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:91:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_groups_ioe             = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:92:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_cluster_vec_local      = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:93:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_cluster_log_local      = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:151:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it.baseName, it ] }
                        ^^
```
Warning: subworkflows/local/suppa.nf:151:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it.baseName, it ] }
                                     ^^
```

Warning: subworkflows/local/suppa.nf:167:26: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .map { [ it.baseName.toString().replaceAll("local_", ""), it ] }
                         ^^

Warning: subworkflows/local/suppa.nf:167:75: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .map { [ it.baseName.toString().replaceAll("local_", ""), it ] }
                                                                          ^^

Warning: subworkflows/local/suppa.nf:181:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_tpms = ch_suppa_local_contrasts.map { [ it.treatment, it.control, it.tpm1, it.tpm2 ] }
                                                                   ^^

Warning: subworkflows/local/suppa.nf:181:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_tpms = ch_suppa_local_contrasts.map { [ it.treatment, it.control, it.tpm1, it.tpm2 ] }
                                                                                 ^^

Warning: subworkflows/local/suppa.nf:181:94: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_tpms = ch_suppa_local_contrasts.map { [ it.treatment, it.control, it.tpm1, it.tpm2 ] }
                                                                                             ^^

Warning: subworkflows/local/suppa.nf:181:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_tpms = ch_suppa_local_contrasts.map { [ it.treatment, it.control, it.tpm1, it.tpm2 ] }
                                                                                                      ^^

Warning: subworkflows/local/suppa.nf:183:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_local_psi = ch_suppa_local_contrasts.map { [ it.treatment, it.control, it.psi1, it.psi2 ] }
                                                                        ^^

Warning: subworkflows/local/suppa.nf:183:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_local_psi = ch_suppa_local_contrasts.map { [ it.treatment, it.control, it.psi1, it.psi2 ] }
                                                                                      ^^

Warning: subworkflows/local/suppa.nf:183:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_local_psi = ch_suppa_local_contrasts.map { [ it.treatment, it.control, it.psi1, it.psi2 ] }
                                                                                                  ^^

Warning: subworkflows/local/suppa.nf:183:108: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_local_psi = ch_suppa_local_contrasts.map { [ it.treatment, it.control, it.psi1, it.psi2 ] }
                                                                                                           ^^

Warning: subworkflows/local/suppa.nf:245:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_ioi_events              = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:246:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_suppa_isoform_psi       = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:247:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_split_suppa_isoform_psi = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:249:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_dpsi_isoform            = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:250:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_psivec_isoform          = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:252:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_groups_ioi              = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:253:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_cluster_vec_isoform     = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:254:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_cluster_log_isoform     = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/suppa.nf:311:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it.baseName, it ] }
                        ^^
```
Warning: subworkflows/local/suppa.nf:311:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it.baseName, it ] }
                                     ^^
```

Warning: subworkflows/local/suppa.nf:327:26: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .map { [ it.baseName.toString().replaceAll("transcript_", ""), it ] }
                         ^^

Warning: subworkflows/local/suppa.nf:327:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

                .map { [ it.baseName.toString().replaceAll("transcript_", ""), it ] }
                                                                               ^^

Warning: subworkflows/local/suppa.nf:341:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_tpms = ch_suppa_isoform_contrasts.map { [ it.treatment, it.control, it.tpm1, it.tpm2 ] }
                                                                     ^^

Warning: subworkflows/local/suppa.nf:341:84: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_tpms = ch_suppa_isoform_contrasts.map { [ it.treatment, it.control, it.tpm1, it.tpm2 ] }
                                                                                   ^^

Warning: subworkflows/local/suppa.nf:341:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_tpms = ch_suppa_isoform_contrasts.map { [ it.treatment, it.control, it.tpm1, it.tpm2 ] }
                                                                                               ^^

Warning: subworkflows/local/suppa.nf:341:105: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_tpms = ch_suppa_isoform_contrasts.map { [ it.treatment, it.control, it.tpm1, it.tpm2 ] }
                                                                                                        ^^

Warning: subworkflows/local/suppa.nf:343:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_isoform_psi = ch_suppa_isoform_contrasts.map { [ it.treatment, it.control, it.psi1, it.psi2 ] }
                                                                            ^^

Warning: subworkflows/local/suppa.nf:343:91: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_isoform_psi = ch_suppa_isoform_contrasts.map { [ it.treatment, it.control, it.psi1, it.psi2 ] }
                                                                                          ^^

Warning: subworkflows/local/suppa.nf:343:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_isoform_psi = ch_suppa_isoform_contrasts.map { [ it.treatment, it.control, it.psi1, it.psi2 ] }
                                                                                                      ^^

Warning: subworkflows/local/suppa.nf:343:112: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_split_suppa_isoform_psi = ch_suppa_isoform_contrasts.map { [ it.treatment, it.control, it.psi1, it.psi2 ] }
                                                                                                               ^^

Warning: subworkflows/local/tx2gene_tximport.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/tx2gene_tximport.nf:31:14: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        tar: it[0].tgz == true
             ^^
```
Warning: subworkflows/local/tx2gene_tximport.nf:32:14: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        dir: it[0].tgz == false
             ^^
```
Warning: subworkflows/local/tx2gene_tximport.nf:48:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    TXIMPORT ( salmon_results.collect{it[1]}, tx2gene )
                                      ^^
```
Warning: subworkflows/local/utils_nfcore_rnasplice_pipeline/main.nf:31:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnasplice_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_rnasplice_pipeline/main.nf:71:5: Variable was declared but not used
```
    versions    = ch_versions
    ^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnasplice_pipeline/main.nf:419:22: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, fastq -> meta.single_end }
                     ^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnasplice_pipeline/main.nf:423:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            if (it.size() > 1) {
                ^^
```
Warning: subworkflows/local/utils_nfcore_rnasplice_pipeline/main.nf:434:22: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, fastq -> meta.strandedness }
                     ^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnasplice_pipeline/main.nf:438:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            if (it.size() > 1) {
                ^^
```
Warning: subworkflows/local/visualise_miso.nf:27:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/visualise_miso.nf:71:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_bams = ch_genome_bam.collect({it[1]})
                                     ^^
```
Warning: subworkflows/local/visualise_miso.nf:72:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_miso_run = MISO_RUN.out.miso.map{it[1]}.collect()
                                        ^^
```

Warning: subworkflows/local/visualise_miso.nf:87:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def miso_genes_list = miso_genes ? miso_genes.split(',').collect{ it.trim() } : [""]
                                                                      ^^

Warning: subworkflows/local/visualise_miso.nf:88:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_miso_genes_list = Channel.fromList( miso_genes_list )
                         ^^^^^^^
```
Warning: subworkflows/local/visualise_miso.nf:91:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_miso_genes_file = Channel.fromPath(miso_genes_file)
                             ^^^^^^^
```
Warning: subworkflows/local/visualise_miso.nf:96:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_miso_genes_file = Channel.fromPath(miso_genes_file)
                             ^^^^^^^
```
Warning: subworkflows/local/visualise_miso.nf:105:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[1], it[2] ] }
                ^^
```
Warning: subworkflows/local/visualise_miso.nf:105:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[1], it[2] ] }
                       ^^
```
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/bedgraph_bedclip_bedgraphtobigwig/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_fastqc_umitools_trimgalore/main.nf:35:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:36:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_html = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:37:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_zip  = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:46:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    umi_log   = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:67:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_unpaired   = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:68:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_html       = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:69:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_zip        = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:70:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_log        = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:71:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_read_count = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:99:23: Parameter was not used -- prefix with _ to suppress warning
```
            .filter { meta, reads, num_reads -> num_reads >= min_trimmed_reads.toFloat() }
                      ^^^^
```

Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:99:29: Parameter was not used -- prefix with _ to suppress warning

            .filter { meta, reads, num_reads -> num_reads >= min_trimmed_reads.toFloat() }
                            ^^^^^

Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:100:33: Parameter was not used -- prefix with _ to suppress warning
```
            .map { meta, reads, num_reads -> [ meta, reads ] }
                                ^^^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:104:26: Parameter was not used -- prefix with _ to suppress warning
```
            .map { meta, reads, num_reads -> [ meta, num_reads ] }
                         ^^^^^
```
Warning: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:94:33: Parameter was not used -- prefix with _ to suppress warning
```
    catch (NullPointerException e) {
                                ^
```
Warning: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:98:24: Parameter was not used -- prefix with _ to suppress warning
```
    catch (IOException e) {
                       ^
```

Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:116:98: 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: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:264:22: Parameter was not used -- prefix with _ to suppress warning
```
    catch (Exception all) {
                     ^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:361:26: Parameter was not used -- prefix with _ to suppress warning
```
        catch (Exception all) {
                         ^^^
```

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