Nextflow lint results

Generated: 2026-01-16T10:21:12.551179534Z
Nextflow version: 25.12.0-edge
Summary: 85 errors, 148 warnings

❌ Errors

Error: assets/pasa/alignAssembly.config:2:1: Unexpected character: '#'
```
## templated variables to be replaced exist as <__var_name__>
^
```
Error: assets/pasa/annotationCompare.config:2:1: Unexpected character: '#'
```
## templated variables to be replaced exist as <__var_name__>
^
```

Error: conf/base.config:13:16: check_max is not defined

    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
               ^^^^^^^^^

Error: conf/base.config:14:16: check_max is not defined

    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
               ^^^^^^^^^

Error: conf/base.config:15:16: check_max is not defined

    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
               ^^^^^^^^^

Error: conf/base.config:27:20: check_max is not defined

        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:28:20: check_max is not defined

        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:29:20: check_max is not defined

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:32:20: check_max is not defined

        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:33:20: check_max is not defined

        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:34:20: check_max is not defined

        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:37:20: check_max is not defined

        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:38:20: check_max is not defined

        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:39:20: check_max is not defined

        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:42:20: check_max is not defined

        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:45:20: check_max is not defined

        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:46:20: check_max is not defined

        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:47:20: check_max is not defined

        time   = { check_max( 72.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:50:20: check_max is not defined

        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
                   ^^^^^^^^^

Error: main.nf:28:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
WorkflowMain.initialise(workflow, params, log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: main.nf:28:1: WorkflowMain is not defined

WorkflowMain.initialise(workflow, params, log)
^^^^^^^^^^^^

Error: modules/local/augustus/augustusbatch.nf:11:9: AUGUSTUS_CONFIG_PATH is not defined
```
    env AUGUSTUS_CONFIG_PATH
        ^^^^^^^^^^^^^^^^^^^^
```
Error: modules/local/augustus/training.nf:13:9: AUGUSTUS_CONFIG_PATH is not defined
```
    env AUGUSTUS_CONFIG_PATH
        ^^^^^^^^^^^^^^^^^^^^
```

Error: modules/local/helper/addexons.nf:14:27: models is not defined

    tuple val(meta), path(models), emit: gff
                          ^^^^^^

Error: modules/local/helper/pasa2training.nf:5:5: Invalid process directive
```
    if (params.enable_conda) {
    ^
```
Error: modules/local/kraken.nf:5:5: Invalid process directive
```
    if (params.enable_conda) {
    ^
```
Error: modules/local/pasa/alignassemble.nf:5:5: Invalid process directive
```
    if (params.enable_conda) {
    ^
```
Error: modules/local/pasa/asmblstotraining.nf:5:5: Invalid process directive
```
    if (params.enable_conda) {
    ^
```
Error: modules/local/pasa/seqclean.nf:5:5: Invalid process directive
```
    if (params.enable_conda) {
    ^
```
Error: modules/local/repeatmasker/repeatmask.nf:12:9: LIBDIR is not defined
```
    env LIBDIR
        ^^^^^^
```
Error: modules/local/satsuma2/satsumasynteny2.nf:5:5: Invalid process directive
```
    if (params.enable_conda) {
    ^
```

Error: nextflow.config:120:5: Unexpected input: 'includeConfig'

    includeConfig "${params.custom_config_base}/nfcore_custom.config"
    ^

Error: subworkflows/local/genome_align.nf:98:5: array was assigned but not declared
```
    array = [ meta, file(row.fasta), file(row.gtf) ]
    ^^^^^
```
Error: subworkflows/local/genome_align.nf:100:12: array is not defined
```
    return array
           ^^^^^
```
Error: workflows/genomeannotator.nf:7:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/genomeannotator.nf:7:22: NfcoreSchema is not defined

def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
                     ^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:10:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
WorkflowGenomeannotator.initialise(params, log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:10:1: WorkflowGenomeannotator is not defined
```
WorkflowGenomeannotator.initialise(params, log)
^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:12:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def checkPathParamList = [ params.multiqc_config, params.assembly ]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/genomeannotator.nf:13:1: for loops are no longer supported

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
^^^

Error: workflows/genomeannotator.nf:13:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:13:6: param is not defined

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
     ^^^^^

Error: workflows/genomeannotator.nf:13:40: param is not defined

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
                                       ^^^^^^^

Error: workflows/genomeannotator.nf:13:55: param is not defined

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
                                                      ^^^^^

Error: workflows/genomeannotator.nf:16:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.assembly) { ch_genome = file(params.assembly, checkIfExists: true) } else { exit 1, 'No assembly specified!' }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:19:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.proteins) { ch_proteins = file(params.proteins, checkIfExists: true) } else { ch_proteins = Channel.empty() }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:20:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.proteins_targeted) { ch_proteins_targeted = file(params.proteins_targeted, checkIfExists: true) } else { ch_proteins_targeted = Channel.empty() }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:21:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.transcripts) { ch_t = file(params.transcripts) } else { ch_transcripts = Channel.empty() }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:22:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.rnaseq_samples) { ch_samplesheet = file(params.rnaseq_samples, checkIfExists: true) } else { ch_samplesheet = Channel.empty() }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:23:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.rm_lib) { ch_repeats = Channel.fromPath(file(params.rm_lib, checkIfExists: true)) } else { ch_repeats = Channel.fromPath("${workflow.projectDir}/assets/repeatmasker/repeats.fa") }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:24:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.aug_config_dir) { ch_aug_config_folder = file(params.aug_config_dir, checkIfExists: true) } else { ch_aug_config_folder = Channel.from(params.aug_config_container) }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:25:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.references) { ch_ref_genomes = Channel.fromPath(params.references, checkIfExists: true)  } else { ch_ref_genomes = Channel.empty() }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:26:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.rm_db)  { ch_rm_db = file(params.rm_db) } else { ch_rm_db = Channel.empty() }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:34:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:35:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:36:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_aug_extrinsic_cfg = params.aug_extrinsic_cfg ? Channel.from( file(params.aug_extrinsic_cfg, checkIfExists: true) ) : Channel.from( file("${workflow.projectDir}/assets/augustus/augustus_default.cfg"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:37:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_evm_weights = Channel.from(file(params.evm_weights, checkIfExists: true))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:38:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_rfam_cm = file("${workflow.projectDir}/assets/rfam/14.2/Rfam.cm.gz", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:39:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_rfam_family = file("${workflow.projectDir}/assets/rfam/14.2/family.txt.gz", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:88:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def multiqc_report = []
^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:109:11: ch_t is not defined
```
          ch_t
          ^^^^
```

Error: workflows/genomeannotator.nf:117:26: ch_aug_config_folder is not defined

    AUGUSTUS_STAGECONFIG(ch_aug_config_folder)
                         ^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:124:9: ch_genome is not defined
```
        ch_genome
        ^^^^^^^^^
```
Error: workflows/genomeannotator.nf:134:11: ch_rfam_cm is not defined
```
          ch_rfam_cm,
          ^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:135:11: ch_rfam_family is not defined
```
          ch_rfam_family
          ^^^^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:145:11: ch_ref_genomes is not defined
```
          ch_ref_genomes
          ^^^^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:169:11: ch_rm_db is not defined
```
          ch_rm_db
          ^^^^^^^^
```
Error: workflows/genomeannotator.nf:178:11: ch_rm_db is not defined
```
          ch_rm_db
          ^^^^^^^^
```
Error: workflows/genomeannotator.nf:189:11: ch_proteins is not defined
```
          ch_proteins,
          ^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:202:11: ch_proteins_targeted is not defined
```
          ch_proteins_targeted,
          ^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:216:11: ch_samplesheet is not defined
```
          ch_samplesheet
          ^^^^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:222:9: Variables in a closure should be declared with def
```
        new_meta = [:]
        ^^^^^^^^
```
Error: workflows/genomeannotator.nf:290:11: AUGUSTUS_TRAINING is not defined
```
          AUGUSTUS_TRAINING(
          ^^^^^^^^^^^^^^^^^
```

Error: workflows/genomeannotator.nf:293:33: AUGUSTUS_TRAINING is not defined

          ch_aug_config_final = AUGUSTUS_TRAINING.out.aug_config_folder
                                ^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:295:11: AUGUSTUS_TRAINING is not defined
```
          AUGUSTUS_TRAINING(
          ^^^^^^^^^^^^^^^^^
```

Error: workflows/genomeannotator.nf:298:33: AUGUSTUS_TRAINING is not defined

          ch_aug_config_final = AUGUSTUS_TRAINING.out.aug_config_folder
                                ^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:314:8: ch_aug_extrinsic_cfg is not defined
```
       ch_aug_extrinsic_cfg,
       ^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/genomeannotator.nf:329:11: ch_evm_weights is not defined
```
          ch_evm_weights
          ^^^^^^^^^^^^^^
```

Error: workflows/genomeannotator.nf:357:27: WorkflowGenomeannotator is not defined

    workflow_summary    = WorkflowGenomeannotator.paramsSummaryMultiqc(workflow, summary_params)
                          ^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:357:82: summary_params is not defined

    workflow_summary    = WorkflowGenomeannotator.paramsSummaryMultiqc(workflow, summary_params)
                                                                                 ^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:361:58: ch_multiqc_config is not defined

    ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
                                                         ^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:362:45: ch_multiqc_custom_config is not defined

    ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
                                            ^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:380:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
workflow.onComplete {
^
```

Error: workflows/genomeannotator.nf:382:9: NfcoreTemplate is not defined

        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
        ^^^^^^^^^^^^^^

Error: workflows/genomeannotator.nf:384:5: NfcoreTemplate is not defined

    NfcoreTemplate.summary(workflow, params, log)
    ^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/augustus/aligntohints.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/augustus/aligntohints.nf:22:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/augustus/augustusbatch.nf:22:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/augustus/bam2hints.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/augustus/fixjoingenes.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/augustus/fixjoingenes.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/augustus/stageconfig.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/augustus/training.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/augustus/training.nf:23:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/busco/busco.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/busco/busco.nf:23:9: Variable was declared but not used

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

Warning: modules/local/busco/downloaddb.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/cat/fasta.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/cat/gff.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/evidencemodeler/execute.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/evidencemodeler/execute.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/evidencemodeler/merge.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/evidencemodeler/merge.nf:21:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/evidencemodeler/partition.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/evidencemodeler/partition.nf:25:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/exonerate/fastaclean.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/exonerate/fastaclean.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/fastasplitter.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

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

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

Warning: modules/local/fastp.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/gaas/fastacleaner.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/gaas/fastacleaner.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/gaas/fastafilterbysize.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/gaas/fastastatistics.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/gffread.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/gffread.nf:21:5: Variable was declared but not used
```
    prefix = task.ext.prefix ?: "${meta.id}"
    ^^^^^^
```
Warning: modules/local/helper/addexons.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/bamtogff.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/helper/bamtogff.nf:19:9: Variable was declared but not used

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

Warning: modules/local/helper/creategffids.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/creategffids.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/helper/downloadrfam.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/evm2gff.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/gtf2hints.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/kraken2gff.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/kraken2gff.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/helper/match2gmod.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/match2gmod.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/helper/minimaptohints.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/pasa2training.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/rfamtogff.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/spalntoevm.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/spalntoevm.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/helper/spalntogmod.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/spalntogmod.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/helper/spalntotraining.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/helper/spalntotraining.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/infernal/press.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/infernal/search.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/infernal/search.nf:20:9: Variable was declared but not used

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

Warning: modules/local/kraken.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

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

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

Warning: modules/local/minimap2/align.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/minimap2/align.nf:21:9: Variable was declared but not used

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

Warning: modules/local/pasa/alignassemble.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/pasa/asmblstotraining.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/pasa/asmblstotraining.nf:20:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/pasa/seqclean.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/pasa/seqclean.nf:19:9: Variable was declared but not used

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

Warning: modules/local/repeatmasker/repeatmask.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/repeatmasker/repeatmask.nf:25:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/repeatmasker/stagelib.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/repeatmasker/stagelib.nf:29:13: The use of baseDir in a process is discouraged -- input files should be provided as process inputs
```
       cp ${baseDir}/assets/repeatmasker/my_genome.fa .
            ^^^^^^^
```
Warning: modules/local/repeatmasker/stagelib.nf:30:13: The use of baseDir in a process is discouraged -- input files should be provided as process inputs
```
       cp ${baseDir}/assets/repeatmasker/repeats.fa .
            ^^^^^^^
```
Warning: modules/local/repeatmodeler.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/repeatmodeler.nf:19:9: Variable was declared but not used

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

Warning: modules/local/satsuma2/satsumasynteny2.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/satsuma2/satsumasynteny2.nf:21:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/spaln/align.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/spaln/align.nf:23:9: Variable was declared but not used

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

Warning: modules/local/spaln/makeindex.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/spaln/makeindex.nf:19:9: Variable was declared but not used

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

Warning: modules/local/spaln/merge.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/spaln/merge.nf:21:9: Variable was declared but not used

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

Warning: modules/local/star/align.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/star/index.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/star/index.nf:19:9: Variable was declared but not used

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

Warning: modules/local/trinity/genomeguided.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/trinity/genomeguided.nf:20:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/modules/cat/fastq/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/modules/cat/fastq/main.nf:23:35: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def readList = reads.collect{ it.toString() }
                                  ^^
```
Warning: modules/nf-core/modules/custom/dumpsoftwareversions/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/augustus_pipeline.nf:28:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
       aug_config_folder.collect().map{ it[0].toString() },
                                        ^^
```
Warning: subworkflows/local/augustus_pipeline.nf:50:12: Parameter was not used -- prefix with _ to suppress warning
```
    .map { k,m,f -> tuple(m,f) }
           ^
```
Warning: subworkflows/local/busco_qc.nf:22:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
      ch_lineage_dir = Channel.from([busco_lineage,busco_db_path])
                       ^^^^^^^
```
Warning: subworkflows/local/evm.nf:18:5: Parameter was not used -- prefix with _ to suppress warning
```
    evm_config
    ^^^^^^^^^^
```
Warning: subworkflows/local/genome_align.nf:23:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
       .map { create_target_channel(it) }
                                    ^^
```
Warning: subworkflows/local/genome_align.nf:30:26: Parameter was not used -- prefix with _ to suppress warning
```
       targets.map { m,f,g ->
                         ^
```
Warning: subworkflows/local/genome_align.nf:46:27: Parameter was not used -- prefix with _ to suppress warning
```
          targets.map { m,f,g ->
                          ^
```
Warning: subworkflows/local/genome_align.nf:62:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
       row[1..-1].collect { [row[0].clone(), it]  }
                                             ^^
```
Warning: subworkflows/local/input_check.nf:15:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_fastq_channel(it) }
                                    ^^
```
Warning: subworkflows/local/ncrna.nf:29:38: Parameter was not used -- prefix with _ to suppress warning
```
      GUNZIP_RFAM_CM.out.gunzip.map {m,f -> f}
                                     ^
```
Warning: subworkflows/local/ncrna.nf:50:12: Parameter was not used -- prefix with _ to suppress warning
```
    .map { k,m,f -> tuple(m,f) }
           ^
```
Warning: subworkflows/local/ncrna.nf:55:41: Parameter was not used -- prefix with _ to suppress warning
```
      GUNZIP_RFAM_FAMILY.out.gunzip.map{m,f -> f}
                                        ^
```
Warning: subworkflows/local/repeatmasker.nf:26:31: Parameter was not used -- prefix with _ to suppress warning
```
       GUNZIP.out.gunzip.map {m,g -> g}
                              ^
```

Warning: subworkflows/local/repeatmasker.nf:30:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

       REPEATMASKER_STAGELIB.out.library.collect().map{it[0].toString()},
                                                       ^^

Warning: subworkflows/local/rnaseq_align.nf:25:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_fastq_channel(it) }
                                    ^^
```
Warning: subworkflows/local/rnaseq_align.nf:61:8: The use of Channel to access channel factories is deprecated -- use channel instead
```
       Channel.from(params.dummy_gff).collect(),
       ^^^^^^^
```

Warning: workflows/genomeannotator.nf:16:24: Variable was declared but not used

if (params.assembly) { ch_genome = file(params.assembly, checkIfExists: true) } else { exit 1, 'No assembly specified!' }
                       ^^^^^^^^^

Warning: workflows/genomeannotator.nf:19:104: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.proteins) { ch_proteins = file(params.proteins, checkIfExists: true) } else { ch_proteins = Channel.empty() }
                                                                                                       ^^^^^^^

Warning: workflows/genomeannotator.nf:20:140: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.proteins_targeted) { ch_proteins_targeted = file(params.proteins_targeted, checkIfExists: true) } else { ch_proteins_targeted = Channel.empty() }
                                                                                                                                           ^^^^^^^

Warning: workflows/genomeannotator.nf:21:27: Variable was declared but not used

if (params.transcripts) { ch_t = file(params.transcripts) } else { ch_transcripts = Channel.empty() }
                          ^^^^

Warning: workflows/genomeannotator.nf:21:68: Variable was declared but not used

if (params.transcripts) { ch_t = file(params.transcripts) } else { ch_transcripts = Channel.empty() }
                                                                   ^^^^^^^^^^^^^^

Warning: workflows/genomeannotator.nf:21:85: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.transcripts) { ch_t = file(params.transcripts) } else { ch_transcripts = Channel.empty() }
                                                                                    ^^^^^^^

Warning: workflows/genomeannotator.nf:22:122: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.rnaseq_samples) { ch_samplesheet = file(params.rnaseq_samples, checkIfExists: true) } else { ch_samplesheet = Channel.empty() }
                                                                                                                         ^^^^^^^

Warning: workflows/genomeannotator.nf:23:35: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.rm_lib) { ch_repeats = Channel.fromPath(file(params.rm_lib, checkIfExists: true)) } else { ch_repeats = Channel.fromPath("${workflow.projectDir}/assets/repeatmasker/repeats.fa") }
                                  ^^^^^^^

Warning: workflows/genomeannotator.nf:23:116: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.rm_lib) { ch_repeats = Channel.fromPath(file(params.rm_lib, checkIfExists: true)) } else { ch_repeats = Channel.fromPath("${workflow.projectDir}/assets/repeatmasker/repeats.fa") }
                                                                                                                   ^^^^^^^

Warning: workflows/genomeannotator.nf:24:134: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.aug_config_dir) { ch_aug_config_folder = file(params.aug_config_dir, checkIfExists: true) } else { ch_aug_config_folder = Channel.from(params.aug_config_container) }
                                                                                                                                     ^^^^^^^

Warning: workflows/genomeannotator.nf:25:43: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.references) { ch_ref_genomes = Channel.fromPath(params.references, checkIfExists: true)  } else { ch_ref_genomes = Channel.empty() }
                                          ^^^^^^^

Warning: workflows/genomeannotator.nf:25:127: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.references) { ch_ref_genomes = Channel.fromPath(params.references, checkIfExists: true)  } else { ch_ref_genomes = Channel.empty() }
                                                                                                                              ^^^^^^^

Warning: workflows/genomeannotator.nf:26:72: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.rm_db)  { ch_rm_db = file(params.rm_db) } else { ch_rm_db = Channel.empty() }
                                                                       ^^^^^^^

Warning: workflows/genomeannotator.nf:34:1: Variable was declared but not used

ch_multiqc_config        = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
^^^^^^^^^^^^^^^^^

Warning: workflows/genomeannotator.nf:35:1: Variable was declared but not used

ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/genomeannotator.nf:35:52: The use of Channel to access channel factories is deprecated -- use channel instead

ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
                                                   ^^^^^^^

Warning: workflows/genomeannotator.nf:35:94: The use of Channel to access channel factories is deprecated -- use channel instead

ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
                                                                                             ^^^^^^^

Warning: workflows/genomeannotator.nf:36:1: Variable was declared but not used

ch_aug_extrinsic_cfg = params.aug_extrinsic_cfg ? Channel.from( file(params.aug_extrinsic_cfg, checkIfExists: true) ) : Channel.from( file("${workflow.projectDir}/assets/augustus/augustus_default.cfg"))
^^^^^^^^^^^^^^^^^^^^

Warning: workflows/genomeannotator.nf:36:51: The use of Channel to access channel factories is deprecated -- use channel instead

ch_aug_extrinsic_cfg = params.aug_extrinsic_cfg ? Channel.from( file(params.aug_extrinsic_cfg, checkIfExists: true) ) : Channel.from( file("${workflow.projectDir}/assets/augustus/augustus_default.cfg"))
                                                  ^^^^^^^

Warning: workflows/genomeannotator.nf:36:121: The use of Channel to access channel factories is deprecated -- use channel instead

ch_aug_extrinsic_cfg = params.aug_extrinsic_cfg ? Channel.from( file(params.aug_extrinsic_cfg, checkIfExists: true) ) : Channel.from( file("${workflow.projectDir}/assets/augustus/augustus_default.cfg"))
                                                                                                                        ^^^^^^^

Warning: workflows/genomeannotator.nf:37:1: Variable was declared but not used

ch_evm_weights = Channel.from(file(params.evm_weights, checkIfExists: true))
^^^^^^^^^^^^^^

Warning: workflows/genomeannotator.nf:37:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_evm_weights = Channel.from(file(params.evm_weights, checkIfExists: true))
                 ^^^^^^^
```

Warning: workflows/genomeannotator.nf:38:1: Variable was declared but not used

ch_rfam_cm = file("${workflow.projectDir}/assets/rfam/14.2/Rfam.cm.gz", checkIfExists: true)
^^^^^^^^^^

Warning: workflows/genomeannotator.nf:39:1: Variable was declared but not used

ch_rfam_family = file("${workflow.projectDir}/assets/rfam/14.2/family.txt.gz", checkIfExists: true)
^^^^^^^^^^^^^^

Warning: workflows/genomeannotator.nf:92:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_empty_gff = Channel.fromPath(params.dummy_gff)
                   ^^^^^^^
```
Warning: workflows/genomeannotator.nf:93:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/genomeannotator.nf:94:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_hints = Channel.empty()
               ^^^^^^^
```
Warning: workflows/genomeannotator.nf:95:5: Variable was declared but not used
```
    ch_repeats_lib = Channel.empty()
    ^^^^^^^^^^^^^^
```
Warning: workflows/genomeannotator.nf:95:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_repeats_lib = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/genomeannotator.nf:96:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_proteins_gff = Channel.from([])
                      ^^^^^^^
```
Warning: workflows/genomeannotator.nf:97:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_transcripts_gff = Channel.from([])
                         ^^^^^^^
```
Warning: workflows/genomeannotator.nf:98:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genes_gff = Channel.empty()
                   ^^^^^^^
```
Warning: workflows/genomeannotator.nf:99:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_transcripts = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/genomeannotator.nf:100:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_rm = Channel.empty()
                   ^^^^^^^
```
Warning: workflows/genomeannotator.nf:101:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_proteins_fa = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/genomeannotator.nf:102:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_busco_qc = Channel.empty()
                  ^^^^^^^
```

Warning: workflows/genomeannotator.nf:159:50: Parameter was not used -- prefix with _ to suppress warning

       ch_repeats = REPEATMODELER.out.fasta.map {m,fasta -> fasta}
                                                 ^

Warning: workflows/genomeannotator.nf:274:33: Parameter was not used -- prefix with _ to suppress warning

           ch_transcripts.map { m,t -> t }.collectFile(name: "transcripts.merged.fa").map { it ->
                                ^

Warning: workflows/genomeannotator.nf:326:28: Parameter was not used -- prefix with _ to suppress warning

          ch_genes_gff.map{m,g -> g}.collectFile(name: 'genes.gff3'),
                           ^

Warning: workflows/genomeannotator.nf:327:31: Parameter was not used -- prefix with _ to suppress warning

          ch_proteins_gff.map{m,p -> p}.mix(ch_empty_gff).collectFile(name: 'proteins.gff3'),
                              ^

Warning: workflows/genomeannotator.nf:328:34: Parameter was not used -- prefix with _ to suppress warning

          ch_transcripts_gff.map{m,t ->t}.mix(ch_empty_gff).collectFile(name: 'transcripts.gff3'),
                                 ^

Warning: workflows/genomeannotator.nf:358:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(workflow_summary)
                          ^^^^^^^
```
Warning: workflows/genomeannotator.nf:360:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/genomeannotator.nf:361:45: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config))
                                            ^^^^^^^

Warning: workflows/genomeannotator.nf:370:5: Variable was declared but not used
```
    multiqc_report = MULTIQC.out.report.toList()
    ^^^^^^^^^^^^^^
```

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