Nextflow lint results

Generated: 2026-03-18T00:25:26.348379678Z
Nextflow version: 26.02.0-edge
Summary: 59 errors, 152 warnings

❌ Errors

Error: conf/modules.config:389:5: Unexpected input: '}'
```
    }
    ^
```

Error: modules/local/diamond/blastp/main.nf:36:15: Unexpected input: ':'

        case 0:   out_ext = "blast"; break
              ^

Error: modules/local/eggnog/download/main.nf:1:1: Invalid process definition -- check for missing or out-of-order section labels
```
process EGGNOG_DOWNLOAD {
^
```

Error: modules/nf-core/samtools/sort/main.nf:68:9: reference is already declared

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

Error: modules/nf-core/taxonkit/lineage/main.nf:44:13: prefix is not defined
```
    touch ${prefix}.tsv
            ^^^^^^
```
Error: subworkflows/local/eggnog/main.nf:5:1: Included name 'EGGNOG_DOWNLOAD' is not defined in module '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/metatdenovo/modules/local/eggnog/download/main.nf'
```
include { EGGNOG_DOWNLOAD } from '../../../modules/local/eggnog/download/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/eggnog/main.nf:17:5: EGGNOG_DOWNLOAD is not defined
```
    EGGNOG_DOWNLOAD()
    ^^^^^^^^^^^^^^^
```

Error: subworkflows/local/eggnog/main.nf:18:35: EGGNOG_DOWNLOAD is not defined

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

Error: subworkflows/local/eggnog/main.nf:20:5: EGGNOG_DOWNLOAD is not defined
```
    EGGNOG_DOWNLOAD.out.eggnog_db
    ^^^^^^^^^^^^^^^
```

Error: subworkflows/local/eggnog/main.nf:21:18: EGGNOG_DOWNLOAD is not defined

        .combine(EGGNOG_DOWNLOAD.out.dmnd)
                 ^^^^^^^^^^^^^^^

Error: subworkflows/local/eggnog/main.nf:22:18: EGGNOG_DOWNLOAD is not defined

        .combine(EGGNOG_DOWNLOAD.out.taxa_db)
                 ^^^^^^^^^^^^^^^

Error: subworkflows/local/eggnog/main.nf:23:18: EGGNOG_DOWNLOAD is not defined

        .combine(EGGNOG_DOWNLOAD.out.pkl)
                 ^^^^^^^^^^^^^^^

Error: subworkflows/local/hmmclassify/main.nf:36:5: Every emit must be assigned to a name when there are multiple emits
```
    HMMRANK.out.hmmrank
    ^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/prokka/subsets/main.nf:19:33: contigs is already declared

    PROKKA ( contigs.map{ meta, contigs -> contigs }.splitFasta(size: batchsize, file: true).map { contigs -> [ [ id: contigs.getBaseName() ], contigs] }, [], []  )
                                ^^^^^^^

Error: subworkflows/local/prokka/subsets/main.nf:19:100: contigs is already declared

    PROKKA ( contigs.map{ meta, contigs -> contigs }.splitFasta(size: batchsize, file: true).map { contigs -> [ [ id: contigs.getBaseName() ], contigs] }, [], []  )
                                                                                                   ^^^^^^^

Error: subworkflows/local/prokka/subsets/main.nf:22:24: contigs is already declared

    contigs.map{ meta, contigs -> [ id:"${meta.id}.prokka" ] }
                       ^^^^^^^

Error: subworkflows/local/prokka/subsets/main.nf:28:24: contigs is already declared

    contigs.map{ meta, contigs -> [ id:"${meta.id}.prokka" ] }
                       ^^^^^^^

Error: subworkflows/local/prokka/subsets/main.nf:34:24: contigs is already declared

    contigs.map{ meta, contigs -> [ id:"${meta.id}.prokka" ] }
                       ^^^^^^^

Error: workflows/metatdenovo.nf:3:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if ( ( params.assembler && params.user_assembly ) || ( ! params.assembler && ! params.user_assembly ) ) {
^
```
Error: workflows/metatdenovo.nf:6:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if ( ( params.orf_caller && ( params.user_orfs_gff ) ) && ( ! params.orf_caller && ! params.user_orfs_gff ) ) {
^
```
Error: workflows/metatdenovo.nf:11:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if ( params.user_orfs_gff && ! params.user_orfs_faa ) {
^
```
Error: workflows/metatdenovo.nf:18:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if ( params.assembler && ( params.user_orfs_gff || params.user_orfs_faa ) ) {
^
```
Error: workflows/metatdenovo.nf:23:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
assembler     = params.assembler
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/metatdenovo.nf:24:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
assembly_name = params.assembler ?: params.user_assembly_name
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/metatdenovo.nf:27:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
orf_caller = params.orf_caller
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/metatdenovo.nf:28:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
orfs_name  = params.orf_caller ?: params.user_orfs_name
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/metatdenovo.nf:31:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_multiqc_files = Channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/metatdenovo.nf:35:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_hmmrs = Channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/metatdenovo.nf:36:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if ( params.hmmdir ) {
^
```

Error: workflows/metatdenovo.nf:58:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/metatdenovo/modules/local/diamond/blastp/main.nf'

include { DIAMOND_BLASTP as DIAMOND_TAXONOMY } from '../modules/local/diamond/blastp/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:239:22: fwd is already declared

        .map { meta, fwd, rev -> [ meta, [ fwd, rev ] ] }
                     ^^^

Error: workflows/metatdenovo.nf:239:27: rev is already declared

        .map { meta, fwd, rev -> [ meta, [ fwd, rev ] ] }
                          ^^^

Error: workflows/metatdenovo.nf:259:26: assembly_name is not defined

        .map { [ [ id:"${assembly_name}.${orfs_name}" ], it ] }
                         ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:259:43: orfs_name is not defined

        .map { [ [ id:"${assembly_name}.${orfs_name}" ], it ] }
                                          ^^^^^^^^^

Error: workflows/metatdenovo.nf:345:34: assembly_name is not defined

                .value ( [ [ id: assembly_name ], file(params.user_assembly) ] )
                                 ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:347:17: assembler is not defined

    } else if ( assembler == 'spades' ) {
                ^^^^^^^^^

Error: workflows/metatdenovo.nf:359:34: assembly_name is not defined

            .map { it -> [ [ id: assembly_name ], it, [], [] ] }
                                 ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:374:17: assembler is not defined

    } else if ( assembler == 'megahit' ) {
                ^^^^^^^^^

Error: workflows/metatdenovo.nf:381:34: assembly_name is not defined

            .map { it -> [ [ id: assembly_name ], it ] }
                                 ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:418:10: orf_caller is not defined

    if ( orf_caller == 'prodigal' ) {
         ^^^^^^^^^^

Error: workflows/metatdenovo.nf:419:72: assembly_name is not defined

        PRODIGAL( ch_assembly_contigs.map { meta, contigs -> [ [id: "${assembly_name}.${orfs_name}"], contigs  ] } )
                                                                       ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:419:89: orfs_name is not defined

        PRODIGAL( ch_assembly_contigs.map { meta, contigs -> [ [id: "${assembly_name}.${orfs_name}"], contigs  ] } )
                                                                                        ^^^^^^^^^

Error: workflows/metatdenovo.nf:432:10: orf_caller is not defined

    if ( orf_caller == 'transdecoder' ) {
         ^^^^^^^^^^

Error: workflows/metatdenovo.nf:433:77: assembly_name is not defined

        TRANSDECODER ( ch_assembly_contigs.map { meta, contigs -> [ [id: "${assembly_name}.${orfs_name}" ], contigs ] } )
                                                                            ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:433:94: orfs_name is not defined

        TRANSDECODER ( ch_assembly_contigs.map { meta, contigs -> [ [id: "${assembly_name}.${orfs_name}" ], contigs ] } )
                                                                                             ^^^^^^^^^

Error: workflows/metatdenovo.nf:450:45: assembly_name is not defined

        ch_gff = Channel.value ( [ [ id: "${assembly_name}.${orfs_name}" ], file(params.user_orfs_gff) ] )
                                            ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:450:62: orfs_name is not defined

        ch_gff = Channel.value ( [ [ id: "${assembly_name}.${orfs_name}" ], file(params.user_orfs_gff) ] )
                                                             ^^^^^^^^^

Error: workflows/metatdenovo.nf:451:49: assembly_name is not defined

        ch_protein = Channel.value ( [ [ id: "${assembly_name}.${orfs_name}" ], file(params.user_orfs_faa) ] )
                                                ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:451:66: orfs_name is not defined

        ch_protein = Channel.value ( [ [ id: "${assembly_name}.${orfs_name}" ], file(params.user_orfs_faa) ] )
                                                                 ^^^^^^^^^

Error: workflows/metatdenovo.nf:469:22: ch_hmmrs is not defined

    ch_hmmclassify = ch_hmmrs
                     ^^^^^^^^

Error: workflows/metatdenovo.nf:471:48: assembly_name is not defined

        .map { hmm, meta, protein ->[ [ id: "${assembly_name}.${orfs_name}" ], hmm, protein ] }
                                               ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:471:65: orfs_name is not defined

        .map { hmm, meta, protein ->[ [ id: "${assembly_name}.${orfs_name}" ], hmm, protein ] }
                                                                ^^^^^^^^^

Error: workflows/metatdenovo.nf:496:43: assembly_name is not defined

        .map { featurecounts -> [ [ id:"${assembly_name}.${orfs_name}" ], featurecounts ] }
                                          ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:496:60: orfs_name is not defined

        .map { featurecounts -> [ [ id:"${assembly_name}.${orfs_name}" ], featurecounts ] }
                                                           ^^^^^^^^^

Error: workflows/metatdenovo.nf:568:5: DIAMOND_TAXONOMY is not defined
```
    DIAMOND_TAXONOMY(
    ^^^^^^^^^^^^^^^^
```

Error: workflows/metatdenovo.nf:574:39: DIAMOND_TAXONOMY is not defined

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

Error: workflows/metatdenovo.nf:578:27: DIAMOND_TAXONOMY is not defined

    ch_taxonkit_lineage = DIAMOND_TAXONOMY.out.tsv
                          ^^^^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:627:37: assembly_name is not defined

            .map { it -> [ [ id: "${assembly_name}.${orfs_name}" ], it ] }
                                    ^^^^^^^^^^^^^

Error: workflows/metatdenovo.nf:627:54: orfs_name is not defined

            .map { it -> [ [ id: "${assembly_name}.${orfs_name}" ], it ] }
                                                     ^^^^^^^^^

⚠️ Warnings

Warning: modules/local/collect/featurecounts/main.nf:21:9: Variable was declared but not used
```
    def args     = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/collect/stats/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/collect/stats/main.nf:22:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/diamond/format_tax/ranklist/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/diamond/format_tax/taxdump/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/eggnog/sum/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/eggnog/sum/main.nf:25:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/eukulele/format_tax/main.nf:21:9: Variable was declared but not used
```
    def args   = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/format/prodigal/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```
Warning: modules/local/format/prodigal/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```
Warning: modules/local/format/spades/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/format/spades/main.nf:22:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/kofamscan/download/main.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/kofamscan/scan/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/kofamscan/scan/main.nf:25:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/kofamscan/sum/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/kofamscan/sum/main.nf:23:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/kofamscan/unique/main.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/kofamscan/unique/main.nf:54:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/megahit/interleaved/main.nf:27:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: ''
        ^^^^^^
```
Warning: modules/local/megahit/interleaved/main.nf:53:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: ''
        ^^^^^^
```
Warning: modules/local/merge/summary/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/prokka/gff2tsv/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/seqtk/hmmhitfaas/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/seqtk/hmmhitfaas/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/spades/writeyaml/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/sumtaxonomy/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bbmap/bbduk/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/cat/cat/main.nf:23:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list = files_in.collect { it.toString() }
                                       ^^
```
Warning: modules/nf-core/cat/cat/main.nf:58:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list   = files_in.collect { it.toString() }
                                         ^^
```

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

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

Warning: modules/nf-core/cat/fastq/main.nf:77:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: modules/nf-core/pigz/compress/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/prodigal/main.nf:49:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```

Warning: modules/nf-core/samtools/sort/main.nf:68:9: Variable was declared but not used

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

Warning: modules/nf-core/spades/main.nf:80:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/spades/main.nf:82:9: Variable was declared but not used
```
    def maxmem = task.memory.toGiga()
        ^^^^^^
```

Warning: modules/nf-core/spades/main.nf:86:9: Variable was declared but not used

    def custom_hmms = hmm ? "--custom-hmms $hmm" : ""
        ^^^^^^^^^^^

Warning: modules/nf-core/spades/main.nf:87:9: Variable was declared but not used

    def reads = yml ? "--dataset $yml" : "$illumina_reads $pacbio_reads $nanopore_reads"
        ^^^^^

Warning: modules/nf-core/trimgalore/main.nf:47:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        args_list.removeAll { it.toLowerCase().contains('_r2 ') }
                              ^^
```
Warning: subworkflows/local/eggnog/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/eukulele/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/eukulele/main.nf:21:88: Parameter was not used -- prefix with _ to suppress warning

    FORMAT_EUKULELE_TAX( EUKULELE_SEARCH.out.taxonomy_estimation.map { meta, taxonomy, dbname -> [ meta, taxonomy ] } )
                                                                                       ^^^^^^

Warning: subworkflows/local/eukulele/main.nf:26:32: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, taxonomy, protein, dbname, database -> [ meta, dbname, taxonomy ] }
                               ^^^^^^^

Warning: subworkflows/local/eukulele/main.nf:26:49: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, taxonomy, protein, dbname, database -> [ meta, dbname, taxonomy ] }
                                                ^^^^^^^^

Warning: subworkflows/local/fastqc/trimgalore/main.nf:15:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/fastqc/trimgalore/main.nf:16:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_html    = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/fastqc/trimgalore/main.nf:17:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_zip     = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/fastqc/trimgalore/main.nf:26:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_html  = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/fastqc/trimgalore/main.nf:27:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_zip   = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/fastqc/trimgalore/main.nf:28:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_log   = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/hmmclassify/main.nf:11:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/hmmclassify/main.nf:21:26: Parameter was not used -- prefix with _ to suppress warning
```
            .map { meta, hmm, seqdb -> meta }
                         ^^^
```
Warning: subworkflows/local/hmmclassify/main.nf:21:31: Parameter was not used -- prefix with _ to suppress warning
```
            .map { meta, hmm, seqdb -> meta }
                              ^^^^^
```

Warning: subworkflows/local/hmmclassify/main.nf:23:69: Parameter was not used -- prefix with _ to suppress warning

            .combine ( HMMER_HMMSEARCH.out.target_summary.collect { meta, summary -> summary } )
                                                                    ^^^^

Warning: subworkflows/local/hmmclassify/main.nf:24:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [ it[0], it[1..-1] ] }
                     ^^
```
Warning: subworkflows/local/hmmclassify/main.nf:24:29: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [ it[0], it[1..-1] ] }
                            ^^
```

Warning: subworkflows/local/hmmclassify/main.nf:31:35: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, hmmrank, hmms, faa -> [ meta, hmmrank, faa ] }
                                  ^^^^

Warning: subworkflows/local/kofamscan/main.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prodigal/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prokka/subsets/main.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/prokka/subsets/main.nf:19:27: Parameter was not used -- prefix with _ to suppress warning

    PROKKA ( contigs.map{ meta, contigs -> contigs }.splitFasta(size: batchsize, file: true).map { contigs -> [ [ id: contigs.getBaseName() ], contigs] }, [], []  )
                          ^^^^

Warning: subworkflows/local/prokka/subsets/main.nf:21:36: Parameter was not used -- prefix with _ to suppress warning
```
    ch_log  = PROKKA.out.txt.map { meta, log -> log }.collect()
                                   ^^^^
```
Warning: subworkflows/local/prokka/subsets/main.nf:22:24: Parameter was not used -- prefix with _ to suppress warning
```
    contigs.map{ meta, contigs -> [ id:"${meta.id}.prokka" ] }
                       ^^^^^^^
```

Warning: subworkflows/local/prokka/subsets/main.nf:23:43: Parameter was not used -- prefix with _ to suppress warning

        .combine(PROKKA.out.gff.collect { meta, gff -> gff }.map { [ it ] })
                                          ^^^^

Warning: subworkflows/local/prokka/subsets/main.nf:23:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .combine(PROKKA.out.gff.collect { meta, gff -> gff }.map { [ it ] })
                                                                     ^^

Warning: subworkflows/local/prokka/subsets/main.nf:28:24: Parameter was not used -- prefix with _ to suppress warning
```
    contigs.map{ meta, contigs -> [ id:"${meta.id}.prokka" ] }
                       ^^^^^^^
```

Warning: subworkflows/local/prokka/subsets/main.nf:29:43: Parameter was not used -- prefix with _ to suppress warning

        .combine(PROKKA.out.faa.collect { meta, protein -> protein }.map { [ it ] })
                                          ^^^^

Warning: subworkflows/local/prokka/subsets/main.nf:29:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .combine(PROKKA.out.faa.collect { meta, protein -> protein }.map { [ it ] })
                                                                             ^^

Warning: subworkflows/local/prokka/subsets/main.nf:34:24: Parameter was not used -- prefix with _ to suppress warning
```
    contigs.map{ meta, contigs -> [ id:"${meta.id}.prokka" ] }
                       ^^^^^^^
```

Warning: subworkflows/local/prokka/subsets/main.nf:35:43: Parameter was not used -- prefix with _ to suppress warning

        .combine(PROKKA.out.ffn.collect { meta, fnn -> fnn }.map { [ it ] })
                                          ^^^^

Warning: subworkflows/local/prokka/subsets/main.nf:35:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .combine(PROKKA.out.ffn.collect { meta, fnn -> fnn }.map { [ it ] })
                                                                     ^^

Warning: subworkflows/local/utils_nfcore_metatdenovo_pipeline/main.nf:32:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_metatdenovo_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_metatdenovo_pipeline/main.nf:128:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_diamond_paths = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_metatdenovo_pipeline/main.nf:130:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_diamond_paths = Channel
                           ^^^^^^^
```
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: workflows/metatdenovo.nf:23:1: Variable was declared but not used
```
assembler     = params.assembler
^^^^^^^^^
```

Warning: workflows/metatdenovo.nf:24:1: Variable was declared but not used

assembly_name = params.assembler ?: params.user_assembly_name
^^^^^^^^^^^^^

Warning: workflows/metatdenovo.nf:27:1: Variable was declared but not used
```
orf_caller = params.orf_caller
^^^^^^^^^^
```
Warning: workflows/metatdenovo.nf:28:1: Variable was declared but not used
```
orfs_name  = params.orf_caller ?: params.user_orfs_name
^^^^^^^^^
```
Warning: workflows/metatdenovo.nf:31:1: Variable was declared but not used
```
ch_multiqc_files = Channel.empty()
^^^^^^^^^^^^^^^^
```
Warning: workflows/metatdenovo.nf:31:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_multiqc_files = Channel.empty()
                   ^^^^^^^
```
Warning: workflows/metatdenovo.nf:35:12: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_hmmrs = Channel.empty()
           ^^^^^^^
```
Warning: workflows/metatdenovo.nf:37:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: workflows/metatdenovo.nf:41:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: workflows/metatdenovo.nf:43:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [ file(it) ] }
                      ^^
```
Warning: workflows/metatdenovo.nf:146:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/metatdenovo.nf:147:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/metatdenovo.nf:157:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

                return [[ meta.id, pairs.collect { meta + [id: "${meta.id}_${pairs.indexOf(it) + 1}"] }, fastq_files ]]
                                                                                           ^^

Warning: workflows/metatdenovo.nf:168:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { validateInputSamplesheet(it) }
                                        ^^
```
Warning: workflows/metatdenovo.nf:196:25: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, f -> ! meta.single_end }
                        ^
```
Warning: workflows/metatdenovo.nf:210:25: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, f -> ! meta.single_end }
                        ^
```
Warning: workflows/metatdenovo.nf:224:25: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, f -> meta.single_end }
                        ^
```
Warning: workflows/metatdenovo.nf:258:26: Parameter was not used -- prefix with _ to suppress warning
```
        .collect { meta, fasta -> meta }
                         ^^^^^
```

Warning: workflows/metatdenovo.nf:259:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [ [ id:"${assembly_name}.${orfs_name}" ], it ] }
                                                         ^^

Warning: workflows/metatdenovo.nf:269:32: Parameter was not used -- prefix with _ to suppress warning

                    .collect { meta, report ->
                               ^^^^

Warning: workflows/metatdenovo.nf:276:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    .map { [ it ] }
                             ^^
```

Warning: workflows/metatdenovo.nf:284:52: The use of Channel to access channel factories is deprecated -- use channel instead

        BBMAP_BBDUK ( FASTQC_TRIMGALORE.out.reads, Channel.fromPath(params.sequence_filter).first() )
                                                   ^^^^^^^

Warning: workflows/metatdenovo.nf:286:55: Parameter was not used -- prefix with _ to suppress warning

        ch_bbduk_logs = BBMAP_BBDUK.out.log.collect { meta, log ->  log }.map { [ it ] }
                                                      ^^^^

Warning: workflows/metatdenovo.nf:286:83: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_bbduk_logs = BBMAP_BBDUK.out.log.collect { meta, log ->  log }.map { [ it ] }
                                                                                  ^^

Warning: workflows/metatdenovo.nf:289:78: Parameter was not used -- prefix with _ to suppress warning

        ch_multiqc_files = ch_multiqc_files.mix(BBMAP_BBDUK.out.log.collect{ meta, log -> log })
                                                                             ^^^^

Warning: workflows/metatdenovo.nf:292:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_bbduk_logs = Channel.empty()
                        ^^^^^^^
```
Warning: workflows/metatdenovo.nf:300:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_interleaved = Channel.empty()
                     ^^^^^^^
```

Warning: workflows/metatdenovo.nf:314:32: Parameter was not used -- prefix with _ to suppress warning

                    .collect { meta, fastq -> fastq }
                               ^^^^

Warning: workflows/metatdenovo.nf:315:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    .map { [ [id:'all_samples', single_end:true], it ] }
                                                                  ^^

Warning: workflows/metatdenovo.nf:317:68: Parameter was not used -- prefix with _ to suppress warning

            ch_pe_reads_to_assembly = BBMAP_BBNORM.out.fastq.map { meta, fasta -> fasta }
                                                                   ^^^^

Warning: workflows/metatdenovo.nf:318:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_se_reads_to_assembly = Channel.empty()
                                      ^^^^^^^
```

Warning: workflows/metatdenovo.nf:322:33: Parameter was not used -- prefix with _ to suppress warning

                .filter { meta, fastq -> ! meta.single_end }
                                ^^^^^

Warning: workflows/metatdenovo.nf:323:24: Parameter was not used -- prefix with _ to suppress warning
```
                .map { meta, fastq -> fastq }
                       ^^^^
```

Warning: workflows/metatdenovo.nf:325:33: Parameter was not used -- prefix with _ to suppress warning

                .filter { meta, fastq -> meta.single_end }
                                ^^^^^

Warning: workflows/metatdenovo.nf:326:24: Parameter was not used -- prefix with _ to suppress warning
```
                .map { meta, fastq -> fastq }
                       ^^^^
```
Warning: workflows/metatdenovo.nf:338:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
                Channel
                ^^^^^^^
```

Warning: workflows/metatdenovo.nf:340:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    .map { [ [ id:params.user_assembly ], it ] }
                                                          ^^

Warning: workflows/metatdenovo.nf:344:35: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_assembly_contigs = Channel
                                  ^^^^^^^

Warning: workflows/metatdenovo.nf:397:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gff      = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/metatdenovo.nf:398:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_protein  = Channel.empty()
                  ^^^^^^^
```

Warning: workflows/metatdenovo.nf:419:45: Parameter was not used -- prefix with _ to suppress warning

        PRODIGAL( ch_assembly_contigs.map { meta, contigs -> [ [id: "${assembly_name}.${orfs_name}"], contigs  ] } )
                                            ^^^^

Warning: workflows/metatdenovo.nf:433:50: Parameter was not used -- prefix with _ to suppress warning

        TRANSDECODER ( ch_assembly_contigs.map { meta, contigs -> [ [id: "${assembly_name}.${orfs_name}" ], contigs ] } )
                                                 ^^^^

Warning: workflows/metatdenovo.nf:450:18: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_gff = Channel.value ( [ [ id: "${assembly_name}.${orfs_name}" ], file(params.user_orfs_gff) ] )
                 ^^^^^^^

Warning: workflows/metatdenovo.nf:451:22: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_protein = Channel.value ( [ [ id: "${assembly_name}.${orfs_name}" ], file(params.user_orfs_faa) ] )
                     ^^^^^^^

Warning: workflows/metatdenovo.nf:457:43: Parameter was not used -- prefix with _ to suppress warning

    BBMAP_INDEX(ch_assembly_contigs.map { meta, contigs -> contigs })
                                          ^^^^

Warning: workflows/metatdenovo.nf:471:21: Parameter was not used -- prefix with _ to suppress warning

        .map { hmm, meta, protein ->[ [ id: "${assembly_name}.${orfs_name}" ], hmm, protein ] }
                    ^^^^

Warning: workflows/metatdenovo.nf:483:31: Parameter was not used -- prefix with _ to suppress warning
```
        .combine(ch_gff.map { meta, bam -> bam } )
                              ^^^^
```

Warning: workflows/metatdenovo.nf:486:65: Parameter was not used -- prefix with _ to suppress warning

        .combine(BAM_SORT_STATS_SAMTOOLS.out.idxstats.collect { meta, idxstats -> idxstats }.map { [ it ] } )
                                                                ^^^^

Warning: workflows/metatdenovo.nf:486:102: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .combine(BAM_SORT_STATS_SAMTOOLS.out.idxstats.collect { meta, idxstats -> idxstats }.map { [ it ] } )
                                                                                                     ^^

Warning: workflows/metatdenovo.nf:495:22: Parameter was not used -- prefix with _ to suppress warning
```
        .collect() { meta, featurecounts -> featurecounts }
                     ^^^^
```

Warning: workflows/metatdenovo.nf:500:72: Parameter was not used -- prefix with _ to suppress warning

    ch_fcs_for_stats      = COLLECT_FEATURECOUNTS.out.counts.collect { meta, tsv -> tsv }.map { [ it ] }
                                                                       ^^^^

Warning: workflows/metatdenovo.nf:500:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_fcs_for_stats      = COLLECT_FEATURECOUNTS.out.counts.collect { meta, tsv -> tsv }.map { [ it ] }
                                                                                                  ^^

Warning: workflows/metatdenovo.nf:501:68: Parameter was not used -- prefix with _ to suppress warning

    ch_fcs_for_summary    = COLLECT_FEATURECOUNTS.out.counts.map { meta, tsv -> tsv }
                                                                   ^^^^

Warning: workflows/metatdenovo.nf:505:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_merge_tables = Channel.empty()
                      ^^^^^^^
```

Warning: workflows/metatdenovo.nf:513:75: Parameter was not used -- prefix with _ to suppress warning

        ch_merge_tables = ch_merge_tables.mix ( EGGNOG.out.sumtable.map { meta, tsv -> tsv } )
                                                                          ^^^^

Warning: workflows/metatdenovo.nf:523:87: Parameter was not used -- prefix with _ to suppress warning

        ch_merge_tables = ch_merge_tables.mix ( KOFAMSCAN.out.kofamscan_summary.map { meta, tsv -> tsv } )
                                                                                      ^^^^

Warning: workflows/metatdenovo.nf:540:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_eukulele_db = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/metatdenovo.nf:550:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_eukulele_db = Channel
                             ^^^^^^^
```
Warning: workflows/metatdenovo.nf:552:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [ it, file(params.eukulele_dbpath) ] }
                         ^^
```

Warning: workflows/metatdenovo.nf:554:30: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_eukulele_db = Channel.fromPath(params.eukulele_dbpath, checkIfExists: true)
                             ^^^^^^^

Warning: workflows/metatdenovo.nf:555:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [ [], it ] }
                             ^^
```

Warning: workflows/metatdenovo.nf:562:89: Parameter was not used -- prefix with _ to suppress warning

        ch_merge_tables = ch_merge_tables.mix ( SUB_EUKULELE.out.taxonomy_summary.map { meta, tsv -> tsv } )
                                                                                        ^^^^

Warning: workflows/metatdenovo.nf:570:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_diamond_dbs.map { [ it[0], it[1] ] },
                               ^^
```
Warning: workflows/metatdenovo.nf:570:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_diamond_dbs.map { [ it[0], it[1] ] },
                                      ^^
```

Warning: workflows/metatdenovo.nf:619:87: Parameter was not used -- prefix with _ to suppress warning

    ch_merge_tables = ch_merge_tables.mix ( SUM_DIAMONDTAX.out.taxonomy_summary.map { meta, tsv -> tsv } )
                                                                                      ^^^^

Warning: workflows/metatdenovo.nf:633:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```

Warning: workflows/metatdenovo.nf:634:60: Parameter was not used -- prefix with _ to suppress warning

                .mix ( MERGE_TABLES.out.merged_table.map { meta, tblout -> [ tblout ] } )
                                                           ^^^^

Warning: workflows/metatdenovo.nf:674:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/metatdenovo.nf:677:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/metatdenovo.nf:678:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/metatdenovo.nf:680:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/metatdenovo.nf:681:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/metatdenovo.nf:685:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

Warning: workflows/metatdenovo.nf:691:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

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