Nextflow lint results

Generated: 2026-01-16T10:25:40.310100666Z
Nextflow version: 25.12.0-edge
Summary: 59 errors, 98 warnings

❌ Errors

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

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

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

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

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

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

Error: conf/base.config:30:20: check_max is not defined

        cpus   = { check_max( 1                  , 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:31:20: check_max is not defined

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

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

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

Error: conf/base.config:35:20: check_max is not defined

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

Error: conf/base.config:36:20: check_max is not defined

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

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

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

Error: conf/base.config:40:20: check_max is not defined

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

Error: conf/base.config:41:20: check_max is not defined

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

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

        time   = { check_max( 8.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( 16.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

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

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

Error: conf/base.config:53:20: check_max is not defined

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

Error: conf/test_full.config:26:1: Invalid include source: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/phageannotator/conf/test_data.config'
```
includeConfig 'test_data.config'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: main.nf:28:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/phageannotator/modules/nf-core/multiqc/main.nf'

include { MULTIQC                               } from './modules/nf-core/multiqc/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:43:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/phageannotator/workflows/phageannotator/main.nf'

include { PHAGEANNOTATOR            } from './workflows/phageannotator/main'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:67:5: PHAGEANNOTATOR is not defined
```
    PHAGEANNOTATOR (
    ^^^^^^^^^^^^^^
```

Error: main.nf:73:16: PHAGEANNOTATOR is not defined

    versions = PHAGEANNOTATOR.out.versions
               ^^^^^^^^^^^^^^

Error: main.nf:138:5: MULTIQC is not defined
```
    MULTIQC (
    ^^^^^^^
```

Error: main.nf:145:26: MULTIQC is not defined

    ch_multiqc_report  = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
                         ^^^^^^^

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

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

Error: nextflow.config:151:5: Unexpected input: 'includeConfig'

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

Error: subworkflows/local/fasta_all_v_all_blast/main.nf:25:31: Unexpected input: '='

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

Error: subworkflows/local/fastq_fasta_contig_extension_cobra/main.nf:49:28: Unexpected input: '='
```
                while( line=source.readLine() ) {
                           ^
```
Error: subworkflows/local/utils_nfcore_phageannotator_pipeline/main.nf:14:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/phageannotator/subworkflows/nf-core/utils_nextflow_pipeline/main.nf'
```
include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_phageannotator_pipeline/main.nf:47:5: UTILS_NEXTFLOW_PIPELINE is not defined
```
    UTILS_NEXTFLOW_PIPELINE (
    ^^^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/nf-core/initialise/main.nf:70:13: Nextflow is not defined

            Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
            ^^^^^^^^

Error: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:111:14: Unexpected input: 'i'
```
    for (int i = 0; i < n - 1; i++) {
             ^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:5:1: Groovy import declarations are not supported -- use fully-qualified name inline instead
```
import org.yaml.snakeyaml.Yaml
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:6:1: Groovy import declarations are not supported -- use fully-qualified name inline instead
```
import nextflow.extension.FilesEx
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:37:5: valid_config was assigned but not declared
```
    valid_config = true
    ^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:45:9: valid_config was assigned but not declared
```
        valid_config = false
        ^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:47:12: valid_config is not defined
```
    return valid_config
           ^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:99:17: Yaml is not defined
```
    Yaml yaml = new Yaml()
                ^^^^^^^^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:100:5: versions was assigned but not declared

    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
    ^^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:27: versions is not defined
```
    return yaml.dumpAsMap(versions).trim()
                          ^^^^^^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:131:5: for loops are no longer supported
```
    for (group in summary_params.keySet()) {
    ^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:131:10: group is not defined
```
    for (group in summary_params.keySet()) {
         ^^^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:132:47: group is not defined

        def group_params = summary_params.get(group)  // This gets the parameters of that particular group
                                              ^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:134:68: group is not defined

            summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
                                                                   ^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:136:13: for loops are no longer supported
```
            for (param in group_params.keySet()) {
            ^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:136:18: param is not defined

            for (param in group_params.keySet()) {
                 ^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:137:49: param is not defined

                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
                                                ^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:137:89: param is not defined

                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
                                                                                        ^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:284:5: for loops are no longer supported
```
    for (group in summary_params.keySet()) {
    ^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:284:10: group is not defined
```
    for (group in summary_params.keySet()) {
         ^^^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:285:34: group is not defined

        summary << summary_params[group]
                                 ^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:344:42: GroovyException is not defined

            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
                                         ^^^^^^^^^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:361:5: FilesEx is not defined

    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
    ^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:367:5: FilesEx is not defined

    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
    ^^^^^^^

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:392:5: for loops are no longer supported
```
    for (group in summary_params.keySet()) {
    ^^^
```
Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:392:10: group is not defined
```
    for (group in summary_params.keySet()) {
         ^^^^^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:393:34: group is not defined

        summary << summary_params[group]
                                 ^^^^^^^

Error: tests/nextflow.config:55:1: Invalid include source: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/phageannotator/tests/https:/github.com/nf-core/modules/raw/master/tests/config/test_data.config'
```
includeConfig 'https://github.com/nf-core/modules/raw/master/tests/config/test_data.config'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/phageannotator/main.nf:411:32: Unexpected input: '='

                    while( line=source.readLine() ) {
                               ^

⚠️ Warnings

Warning: main.nf:61:50: Parameter was not used -- prefix with _ to suppress warning

    ch_fastq_gz = samplesheet.map { meta, fastq, fasta -> return [ meta, fastq ] }
                                                 ^^^^^

Warning: main.nf:62:43: Parameter was not used -- prefix with _ to suppress warning

    ch_fasta_gz = samplesheet.map { meta, fastq, fasta -> return [ meta, fasta ] }
                                          ^^^^^

Warning: main.nf:85:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions         = Channel.empty()
                          ^^^^^^^
```
Warning: main.nf:86:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files    = Channel.empty()
                          ^^^^^^^
```

Warning: main.nf:105:68: Parameter was not used -- prefix with _ to suppress warning

        PIPELINE_INITIALISATION.out.samplesheet.map { meta, fastq, fasta -> return [ meta, fastq ] }
                                                                   ^^^^^

Warning: main.nf:107:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
                                                                   ^^

Warning: main.nf:127:45: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
                                            ^^^^^^^

Warning: main.nf:128:69: 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, checkIfExists: true) : Channel.empty()
                                                                    ^^^^^^^

Warning: main.nf:128:132: 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, checkIfExists: true) : Channel.empty()
                                                                                                                                   ^^^^^^^

Warning: main.nf:129:67: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                                  ^^^^^^^

Warning: main.nf:129:128: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                                                                                               ^^^^^^^

Warning: main.nf:131:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: main.nf:133:45: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
                                            ^^^^^^^

Warning: modules/local/anicluster/anicalc/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/anicluster/anicalc/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/anicluster/aniclust/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/anicluster/extractreps/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/anicluster/extractreps/main.nf:39:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/appendscreenhits/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/appendscreenhits/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/coverm/contig/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/extractviralassemblies/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/extractviralassemblies/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/instrain/stb/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/instrain/stb/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mash/paste/main.nf:39:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/qualityfilterviruses/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/seqkit/seq/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/seqkit/seq/main.nf:49:9: Variable was declared but not used

    def endswith = task.ext.suffix ?: "${extension}.gz"
        ^^^^^^^^

Warning: modules/local/viromeqc/install/main.nf:32:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/viromeqc/viromeqc/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/bacphlip/main.nf:23:9: Variable was declared but not used

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

Warning: modules/nf-core/bacphlip/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/bacphlip/main.nf:38:9: Variable was declared but not used

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

Warning: modules/nf-core/blast/blastn/main.nf:52:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/blast/makeblastdb/main.nf:43:9: 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/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/checkv/downloaddatabase/main.nf:32:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/checkv/endtoend/main.nf:48:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/cobrameta/main.nf:66:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/fastqc/main.nf:27:48: Parameter was not used -- prefix with _ to suppress warning

    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
                                               ^^^^^^^^

Warning: modules/nf-core/genomad/download/main.nf:17:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/genomad/endtoend/main.nf:35:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/genomad/endtoend/main.nf:55:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/genomad/endtoend/main.nf:56:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/instrain/compare/main.nf:28:9: Variable was declared but not used
```
    def stb_args = stb_file ? "-s ${stb_file}": ''
        ^^^^^^^^
```
Warning: modules/nf-core/instrain/compare/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/instrain/compare/main.nf:47:9: Variable was declared but not used
```
    def stb_args = stb_file ? "-s ${stb_file}": ''
        ^^^^^^^^
```
Warning: modules/nf-core/instrain/profile/main.nf:52:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/instrain/profile/main.nf:54:9: Variable was declared but not used

    def genes_args = genes_fasta ? "-g ${genes_fasta}": ''
        ^^^^^^^^^^

Warning: modules/nf-core/instrain/profile/main.nf:55:9: Variable was declared but not used
```
    def stb_args = stb_file ? "-s ${stb_file}": ''
        ^^^^^^^^
```
Warning: modules/nf-core/iphop/download/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/iphop/predict/main.nf:26:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/iphop/predict/main.nf:52:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/mash/screen/main.nf:40:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mash/sketch/main.nf:39:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/pharokka/installdatabases/main.nf:31:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/pharokka/pharokka/main.nf:50:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
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/fasta_microdiversity_instrain/main.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/fasta_microdiversity_instrain/main.nf:20:49: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_genome_fasta_nometa = genome_fasta.map { it[1] }.first()
                                                ^^
```
Warning: subworkflows/local/fasta_microdiversity_instrain/main.nf:22:53: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_proteins_fna_nometa = proteins_fna.map { it[1] }.first()
                                                    ^^
```
Warning: subworkflows/local/fasta_microdiversity_instrain/main.nf:27:53: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_stb_file_tsv_nometa = instrain_stb.map { it[1] }.first()
                                                    ^^
```

Warning: subworkflows/local/fasta_microdiversity_instrain/main.nf:41:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_instrain_compare_input = ch_bam_profiles_combined.map { [ [ id:'all_samples' ], it[1], it[2] ] }.groupTuple( sort: 'deep' )
                                                                                       ^^

Warning: subworkflows/local/fasta_microdiversity_instrain/main.nf:41:95: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_instrain_compare_input = ch_bam_profiles_combined.map { [ [ id:'all_samples' ], it[1], it[2] ] }.groupTuple( sort: 'deep' )
                                                                                              ^^

Warning: subworkflows/local/fasta_microdiversity_instrain/main.nf:46:5: Variable was declared but not used

    ch_instrain_compare = INSTRAIN_COMPARE ( ch_instrain_compare_input, ch_stb_file_tsv_nometa ).compare
    ^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/fasta_microdiversity_instrain/main.nf:47:5: Variable was declared but not used

    ch_instrain_comparisons_tsv = INSTRAIN_COMPARE.out.comparisons_table
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/fasta_microdiversity_instrain/main.nf:48:5: Variable was declared but not used
```
    ch_instrain_pooled_snvs_tsv = INSTRAIN_COMPARE.out.pooled_snv
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/fasta_phage_function_pharokka/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/fasta_phage_host_iphop/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/fasta_phage_host_iphop/main.nf:33:217: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_iphop_db = UNTAR ( [ [ id:'iphop_minimal_db' ], file("https://github.com/nf-core/test-datasets/raw/phageannotator/modules/nfcore/iphop/download/Test_db_rw.tar.gz", checkIfExists: true) ] ).untar.map { it[1] }
                                                                                                                                                                                                                        ^^

Warning: subworkflows/local/fasta_phage_host_iphop/main.nf:44:227: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_iphop_partial_input = UNTAR2 ( [ [ id:'iphop_partial_input' ], file("https://github.com/nf-core/test-datasets/raw/phageannotator/modules/nfcore/iphop/predict/iPHoP_data.tar.gz", checkIfExists: true) ] ).untar.map { it[1] }
                                                                                                                                                                                                                                  ^^

Warning: subworkflows/local/fasta_virus_classification_genomad/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/fasta_virus_quality_checkv/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/fasta_virus_quality_checkv/main.nf:32:224: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_checkv_db = UNTAR ( [ [ id:'checkv_minimal_db' ], file("https://github.com/nf-core/test-datasets/raw/phageannotator/modules/nfcore/checkv/endtoend/checkv_minimal_db.tar", checkIfExists: true) ] ).untar.map { it[1] }
                                                                                                                                                                                                                               ^^

Warning: subworkflows/local/fastq_fasta_reference_containment_mash/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/fastq_fasta_reference_containment_mash/main.nf:49:69: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_mash_screen_tsv = MASH_SCREEN ( ch_mash_screen_input.map { [ it[0], it[1] ] }, ch_mash_screen_input.map { [ it[0], it[2] ] } ).screen
                                                                    ^^

Warning: subworkflows/local/fastq_fasta_reference_containment_mash/main.nf:49:76: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_mash_screen_tsv = MASH_SCREEN ( ch_mash_screen_input.map { [ it[0], it[1] ] }, ch_mash_screen_input.map { [ it[0], it[2] ] } ).screen
                                                                           ^^

Warning: subworkflows/local/fastq_fasta_reference_containment_mash/main.nf:49:116: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_mash_screen_tsv = MASH_SCREEN ( ch_mash_screen_input.map { [ it[0], it[1] ] }, ch_mash_screen_input.map { [ it[0], it[2] ] } ).screen
                                                                                                                   ^^

Warning: subworkflows/local/fastq_fasta_reference_containment_mash/main.nf:49:123: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_mash_screen_tsv = MASH_SCREEN ( ch_mash_screen_input.map { [ it[0], it[1] ] }, ch_mash_screen_input.map { [ it[0], it[2] ] } ).screen
                                                                                                                          ^^

Warning: subworkflows/local/fastq_virus_enrichment_viromeqc/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_phageannotator_pipeline/main.nf:38:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_phageannotator_pipeline/main.nf:42:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_phageannotator_pipeline/main.nf:83:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_phageannotator_pipeline/main.nf:95:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            validateInputSamplesheet(it)
                                     ^^
```

Warning: subworkflows/local/utils_nfcore_phageannotator_pipeline/main.nf:164:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
                                      ^^

Warning: subworkflows/nf-core/bam_sort_stats_samtools/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/bam_stats_samtools/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_align_bowtie2/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/initialise/main.nf:164:10: Parameter was not used -- prefix with _ to suppress warning
```
def logo(workflow, monochrome_logs) {
         ^^^^^^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:121:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { processVersionsFromYAML(it) }
                                               ^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:123:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
                .mix(Channel.of(workflowVersionToYAML()))
                     ^^^^^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:264:14: Parameter was not used -- prefix with _ to suppress warning
```
    } catch (all) {
             ^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:350:18: Parameter was not used -- prefix with _ to suppress warning
```
        } catch (all) {
                 ^^^
```

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