Nextflow lint results

Generated: 2026-01-16T10:17:53.673643718Z
Nextflow version: 25.12.0-edge
Summary: 41 errors, 168 warnings

❌ Errors

Error: conf/modules.config:87:17: Unexpected input: ':'

        withName: FASTQC {
                ^

Error: main.nf:34:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (params.datatype == 'yeast'){
^
```
Error: main.nf:49:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (params.genome == 'GRCm38'){
^
```
Error: main.nf:55:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if(!params.containsKey('regions_mask')){
^
```
Error: main.nf:60:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if(!params.containsKey('additional_fasta')){
^
```
Error: main.nf:65:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (!params.containsKey('fasta_index')){
^
```
Error: main.nf:73:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if(!params.containsKey('bwa_index')){
^
```
Error: main.nf:76:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if(!params.containsKey('bwamem2_index')){
^
```
Error: main.nf:79:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if(!params.containsKey('bowtie_index')){
^
```
Error: main.nf:82:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if(!params.containsKey('bowtie2_index')){
^
```
Error: modules/local/callingcardstools/mammals/concatQC/main.nf:12:15: meta is already declared
```
    tuple val(meta), path(barcode_qc_files)
              ^^^^
```

Error: modules/nf-core/bwa/index/main.nf:14:27: bwa is not defined

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

Error: nextflow.config:312:14: Unexpected input: '('
```
def check_max(obj, type) {
             ^
```

Error: subworkflows/local/align.nf:7:37: Unexpected input: '"'

include { SAMTOOLS_SORT      } from "${projectDir}/modules/nf-core/samtools/sort/main"
                                    ^

Error: subworkflows/local/mammals/process_alignments.nf:33:25: fasta is already declared
```
        fasta.map{meta, fasta -> fasta},
                        ^^^^^
```
Error: subworkflows/local/mammals/process_alignments.nf:34:22: fai is already declared
```
        fai.map{meta,fai -> fai} )
                     ^^^
```

Error: subworkflows/local/prepare_genome.nf:33:29: fasta is already declared

            fasta.map{meta, fasta -> fasta}
                            ^^^^^

Error: subworkflows/local/prepare_genome.nf:37:24: fasta is already declared

            .map{meta, fasta -> [[id: 'masked_' + meta.id], fasta]}
                       ^^^^^

Error: subworkflows/local/prepare_genome.nf:52:24: fasta is already declared

            .map{meta, fasta -> [[id: 'concat_' + meta.id], fasta]}
                       ^^^^^

Error: subworkflows/local/prepare_genome.nf:93:47: fasta is already declared

            BOWTIE_BUILD ( ch_fasta.map{meta, fasta -> fasta}  )
                                              ^^^^^

Error: subworkflows/local/utils_nfcore_callingcards_pipeline/main.nf:97:34: True is not defined

                    single_end = True
                                 ^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:48:20: reads is already declared

        .map{meta, reads ->
                   ^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:51:30: barcode_details is already declared

        .map{id, meta, read, barcode_details ->
                             ^^^^^^^^^^^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:72:21: reads is already declared

        .map{ meta, reads ->
                    ^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:89:28: barcode_details is already declared

        .map{meta, pickle, barcode_details ->
                           ^^^^^^^^^^^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:105:19: reads is already declared

            meta, reads ->
                  ^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:109:20: reads is already declared

        .map{meta, reads ->
                   ^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:111:23: reads is already declared

        .filter{meta, reads ->
                      ^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:117:21: reads is already declared

        .map{ meta, reads ->
                    ^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:150:1: Groovy import declarations are not supported -- use fully-qualified name inline instead
```
import nextflow.util.ArrayBag
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/yeast/prepare_reads.nf:243:9: extractDigit is not defined

        extractDigit(a.toString()) <=> extractDigit(b.toString())
        ^^^^^^^^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:243:40: extractDigit is not defined

        extractDigit(a.toString()) <=> extractDigit(b.toString())
                                       ^^^^^^^^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:261:9: extractReadEnd is not defined

        extractReadEnd(a.toString()) <=> extractReadEnd(b.toString())
        ^^^^^^^^^^^^^^

Error: subworkflows/local/yeast/prepare_reads.nf:261:42: extractReadEnd is not defined

        extractReadEnd(a.toString()) <=> extractReadEnd(b.toString())
                                         ^^^^^^^^^^^^^^

Error: subworkflows/local/yeast/process_alignments.nf:27:25: fasta is already declared
```
        fasta.map{meta, fasta -> fasta},
                        ^^^^^
```
Error: subworkflows/local/yeast/process_alignments.nf:28:22: fai is already declared
```
        fai.map{meta,fai -> fai}
                     ^^^
```

Error: workflows/callingcards.nf:10:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/callingcards/subworkflows/local/align.nf'

include { ALIGN                                            } from "../subworkflows/local/align.nf"
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/callingcards.nf:96:5: ALIGN is not defined
```
    ALIGN (
    ^^^^^
```

Error: workflows/callingcards.nf:103:35: ALIGN is not defined

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

Error: workflows/callingcards.nf:115:9: ALIGN is not defined
```
        ALIGN.out.bam
        ^^^^^
```
Error: workflows/callingcards.nf:163:9: ALIGN is not defined
```
        ALIGN.out.bam
        ^^^^^
```

⚠️ Warnings

Warning: main.nf:37:9: Params should be declared at the top-level (i.e. outside the workflow)

        params.regions_mask = "${projectDir}/assets/yeast/igenomes/R64-1-1/regions_mask.bed"
        ^^^^^^

Warning: main.nf:40:9: Params should be declared at the top-level (i.e. outside the workflow)
```
        params.fasta_index = null
        ^^^^^^
```

Warning: main.nf:44:9: Params should be declared at the top-level (i.e. outside the workflow)

        params.additional_fasta = "${projectDir}/assets/yeast/plasmid_sequences.fasta"
        ^^^^^^

Warning: main.nf:51:9: Params should be declared at the top-level (i.e. outside the workflow)
```
        params.bwa_index = getGenomeAttribute(params, 'bwa')
        ^^^^^^
```
Warning: main.nf:56:5: Params should be declared at the top-level (i.e. outside the workflow)
```
    params.regions_mask = null
    ^^^^^^
```
Warning: main.nf:61:5: Params should be declared at the top-level (i.e. outside the workflow)
```
    params.additional_fasta = null
    ^^^^^^
```
Warning: main.nf:66:5: Params should be declared at the top-level (i.e. outside the workflow)
```
    params.fasta_index = null
    ^^^^^^
```
Warning: main.nf:74:5: Params should be declared at the top-level (i.e. outside the workflow)
```
    params.bwa_index = null
    ^^^^^^
```
Warning: main.nf:77:5: Params should be declared at the top-level (i.e. outside the workflow)
```
    params.bwamem2_index = null
    ^^^^^^
```
Warning: main.nf:80:5: Params should be declared at the top-level (i.e. outside the workflow)
```
    params.bowtie_index = null
    ^^^^^^
```
Warning: main.nf:83:5: Params should be declared at the top-level (i.e. outside the workflow)
```
    params.bowtie2_index = null
    ^^^^^^
```

Warning: main.nf:104:20: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: main.nf:111:18: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_gtf = Channel.fromPath(params.gtf, checkIfExists:true).collect()
                 ^^^^^^^

Warning: main.nf:117:13: The use of Channel to access channel factories is deprecated -- use channel instead

            Channel.fromPath(params.regions_mask, checkIfExists: true)
            ^^^^^^^

Warning: main.nf:119:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```

Warning: main.nf:122:13: The use of Channel to access channel factories is deprecated -- use channel instead

            Channel.fromPath(params.additional_fasta, checkIfExists: true).collect() :
            ^^^^^^^

Warning: main.nf:123:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```

Warning: main.nf:126:50: Implicit closure parameter is deprecated, declare an explicit parameter instead

        params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } :
                                                 ^^

Warning: modules/local/callingcardstools/mammals/concatQC/main.nf:11:15: Variable was declared but not used
```
    tuple val(meta), path(qbed_files)
              ^^^^
```
Warning: modules/local/callingcardstools/mammals/concatQC/main.nf:27:9: Variable was declared but not used
```
    def suffix = task.ext.prefix ?: ""
        ^^^^^^
```
Warning: modules/local/callingcardstools/mammals/count_hops/main.nf:28:9: Variable was declared but not used
```
    def args2 = task.ext.args2 ?: ''
        ^^^^^
```
Warning: modules/local/callingcardstools/yeast/count_hops/main.nf:28:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/callingcardstools/yeast/demultiplex/main.nf:25:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```

Warning: modules/local/concatFasta/main.nf:21:9: Variable was declared but not used

    def args        = task.ext.args     ?: ''
        ^^^^

Warning: modules/local/concatFastq/main.nf:20:9: Variable was declared but not used

    def args        = task.ext.args     ?: ''
        ^^^^

Warning: modules/nf-core/bowtie/build/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

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/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/custom/dumpsoftwareversions/main.nf:22:9: 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/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: subworkflows/local/mammals/prepare_reads.nf:18:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions     = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/mammals/prepare_reads.nf:19:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    umi_log         = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/mammals/prepare_reads.nf:20:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_html     = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/mammals/prepare_reads.nf:21:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_zip      = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/mammals/prepare_reads.nf:22:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trimmomatic_log = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/mammals/prepare_reads.nf:30:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_reads = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/mammals/process_alignments.nf:23:5: Parameter was not used -- prefix with _ to suppress warning
```
    ch_gtf                  // [ path(gtf) ]
    ^^^^^^
```
Warning: subworkflows/local/mammals/process_alignments.nf:27:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/mammals/process_alignments.nf:33:19: Parameter was not used -- prefix with _ to suppress warning
```
        fasta.map{meta, fasta -> fasta},
                  ^^^^
```
Warning: subworkflows/local/mammals/process_alignments.nf:34:17: Parameter was not used -- prefix with _ to suppress warning
```
        fai.map{meta,fai -> fai} )
                ^^^^
```
Warning: subworkflows/local/prepare_genome.nf:23:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:24:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bwamem2_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:25:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bwa_index = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:26:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:27:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie_index = Channel.of("")
                      ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:33:23: Parameter was not used -- prefix with _ to suppress warning
```
            fasta.map{meta, fasta -> fasta}
                      ^^^^
```

Warning: subworkflows/local/prepare_genome.nf:67:32: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_bwamem2_index = Channel.of([[id: 'input_genome_index'],params.bwamem2_index]).collect()
                               ^^^^^^^

Warning: subworkflows/local/prepare_genome.nf:77:28: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_bwa_index = Channel.of([[id: 'input_genome_index'],params.bwa_index]).collect()
                           ^^^^^^^

Warning: subworkflows/local/prepare_genome.nf:87:32: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_bowtie2_index = Channel.of([[id: 'input_genome_index'],params.bowtie2_index]).collect()
                               ^^^^^^^

Warning: subworkflows/local/prepare_genome.nf:93:41: Parameter was not used -- prefix with _ to suppress warning

            BOWTIE_BUILD ( ch_fasta.map{meta, fasta -> fasta}  )
                                        ^^^^

Warning: subworkflows/local/prepare_genome.nf:97:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_bowtie_index = Channel.of([params.bowtie_index]).collect()
                              ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:113:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta_index = Channel.of(["",params.fasta_index]).collect()
                         ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_callingcards_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_callingcards_pipeline/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_callingcards_pipeline/main.nf:38:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_callingcards_pipeline/main.nf:76:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel
        ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_callingcards_pipeline/main.nf:91:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel
        ^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:22:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:23:5: Variable was declared but not used
```
    fastqc_html = Channel.empty()
    ^^^^^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:23:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_html = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:24:5: Variable was declared but not used
```
    fastqc_zip  = Channel.empty()
    ^^^^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:24:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_zip  = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:25:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trimmomatic_log = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:28:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    demux_reads = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:29:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    output_reads = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:51:14: Parameter was not used -- prefix with _ to suppress warning
```
        .map{id, meta, read, barcode_details ->
             ^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:111:17: Parameter was not used -- prefix with _ to suppress warning
```
        .filter{meta, reads ->
                ^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:112:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            reads.every {it.size() > 0} }
                         ^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:231:9: Variable was declared but not used
```
    def extractDigit = { String path ->
        ^^^^^^^^^^^^
```
Warning: subworkflows/local/yeast/prepare_reads.nf:249:9: Variable was declared but not used
```
    def extractReadEnd = { String path ->
        ^^^^^^^^^^^^^^
```
Warning: subworkflows/local/yeast/process_alignments.nf:17:5: Parameter was not used -- prefix with _ to suppress warning
```
    ch_gtf         // [ path(gtf) ]
    ^^^^^^
```
Warning: subworkflows/local/yeast/process_alignments.nf:21:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/yeast/process_alignments.nf:27:19: Parameter was not used -- prefix with _ to suppress warning
```
        fasta.map{meta, fasta -> fasta},
                  ^^^^
```
Warning: subworkflows/local/yeast/process_alignments.nf:28:17: Parameter was not used -- prefix with _ to suppress warning
```
        fai.map{meta,fai -> fai}
                ^^^^
```
Warning: subworkflows/local/yeast/process_alignments.nf:51:14: Parameter was not used -- prefix with _ to suppress warning
```
        .map{meta_join, meta, bam, bai ->
             ^^^^^^^^^
```
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_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_bwaaln/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_bwaaln/main.nf:45:42: Parameter was not used -- prefix with _ to suppress warning

                            meta, reads, meta_index, index ->
                                         ^^^^^^^^^^

Warning: subworkflows/nf-core/fastq_align_bwaaln/main.nf:53:57: Parameter was not used -- prefix with _ to suppress warning

    ch_reads_newid = ch_prepped_input.map{ meta, reads, meta_index, index -> [ meta, reads ] }
                                                        ^^^^^^^^^^

Warning: subworkflows/nf-core/fastq_align_bwaaln/main.nf:53:69: Parameter was not used -- prefix with _ to suppress warning

    ch_reads_newid = ch_prepped_input.map{ meta, reads, meta_index, index -> [ meta, reads ] }
                                                                    ^^^^^

Warning: subworkflows/nf-core/fastq_align_bwaaln/main.nf:54:50: Parameter was not used -- prefix with _ to suppress warning

    ch_index_newid = ch_prepped_input.map{ meta, reads, meta_index, index -> [ meta, index ] }
                                                 ^^^^^

Warning: subworkflows/nf-core/fastq_align_bwaaln/main.nf:54:57: Parameter was not used -- prefix with _ to suppress warning

    ch_index_newid = ch_prepped_input.map{ meta, reads, meta_index, index -> [ meta, index ] }
                                                        ^^^^^^^^^^

Warning: subworkflows/nf-core/fastq_align_bwaaln/main.nf:63:35: Parameter was not used -- prefix with _ to suppress warning

                            meta, reads, sai ->
                                  ^^^^^

Warning: subworkflows/nf-core/fastq_align_bwaaln/main.nf:63:42: Parameter was not used -- prefix with _ to suppress warning

                            meta, reads, sai ->
                                         ^^^

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/callingcards.nf:39:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions          = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/callingcards.nf:40:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files     = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/callingcards.nf:41:5: Variable was declared but not used
```
    ch_fasta_index       = Channel.empty()
    ^^^^^^^^^^^^^^
```
Warning: workflows/callingcards.nf:41:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta_index       = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/callingcards.nf:42:5: Variable was declared but not used
```
    ch_bam_index         = Channel.empty()
    ^^^^^^^^^^^^
```
Warning: workflows/callingcards.nf:42:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bam_index         = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/callingcards.nf:43:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_prepared_reads    = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/callingcards.nf:44:5: Variable was declared but not used
```
    ch_samtools_stats    = Channel.empty()
    ^^^^^^^^^^^^^^^^^
```
Warning: workflows/callingcards.nf:44:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_stats    = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/callingcards.nf:45:5: Variable was declared but not used
```
    ch_samtools_flatstat = Channel.empty()
    ^^^^^^^^^^^^^^^^^^^^
```
Warning: workflows/callingcards.nf:45:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_flatstat = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/callingcards.nf:46:5: Variable was declared but not used
```
    ch_samtools_idxstats = Channel.empty()
    ^^^^^^^^^^^^^^^^^^^^
```
Warning: workflows/callingcards.nf:46:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_idxstats = Channel.empty()
                           ^^^^^^^
```

Warning: workflows/callingcards.nf:77:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:78:97: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:79:98: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:89:94: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:90:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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

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

Warning: workflows/callingcards.nf:119:19: Parameter was not used -- prefix with _ to suppress warning

            .map{ key, meta, bam, bai, barcode_details ->
                  ^^^

Warning: workflows/callingcards.nf:147:101: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:148:104: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:149:104: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:150:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:151:100: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:152:108: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:153:106: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:154:109: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:155:108: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:156:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:169:18: Parameter was not used -- prefix with _ to suppress warning

            .map{id, meta, bam, bai, barcode_details ->
                 ^^

Warning: workflows/callingcards.nf:186:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:187:106: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:188:106: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:189:98: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:190:102: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:191:110: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:192:108: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:193:111: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:194:110: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:195:98: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/callingcards.nf:214:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/callingcards.nf:217:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/callingcards.nf:218:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/callingcards.nf:220:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/callingcards.nf:221:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/callingcards.nf:225:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

Warning: workflows/callingcards.nf:231:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

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