Nextflow lint results

Generated: 2026-02-21T00:19:35.598151083Z
Nextflow version: 26.01.1-edge
Summary: 73 warnings

⚠️ Warnings

Warning: conf/modules.config:592:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { params.run_taxa_classification == false ? it : null },
                                                                ^^

Warning: modules/nf-core/ampcombi2/cluster/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ampcombi2/complete/main.nf:25:49: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        --summaries_files '${summaries.collect{"$it"}.join("' '")}' \\
                                                ^^
```
Warning: modules/nf-core/ampcombi2/complete/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ampcombi2/parsetables/main.nf:43:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        --path_list '${amp_input.collect { "${it}" }.join("' '")}' \\
                                              ^^
```
Warning: modules/nf-core/ampcombi2/parsetables/main.nf:60:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/ampcombi2/parsetables/main.nf:62:9: Variable was declared but not used

    def db_dir = opt_amp_db_dir ? "--amp_database_dir ${opt_amp_db_dir}" : ""
        ^^^^^^

Warning: modules/nf-core/ampcombi2/parsetables/main.nf:63:9: Variable was declared but not used

    def interpro = opt_interproscan ? "--interproscan_output ${opt_interproscan}" : ""
        ^^^^^^^^

Warning: modules/nf-core/ampir/main.nf:25:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ampir/main.nf:49:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/argnorm/main.nf:49:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/deeparg/predict/main.nf:65:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/deepbgc/download/main.nf:17:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/fargene/main.nf:56:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```

Warning: modules/nf-core/gecco/convert/main.nf:27:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}" // IMPORTANT: -o ${prefix} does not work in 0.10.0
        ^^^^^^

Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mmseqs/createdb/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mmseqs/createtsv/main.nf:52:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mmseqs/taxonomy/main.nf:50:9: 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/pyrodigal/main.nf:48:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/amp.nf:111:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            input: [it[0], it[1]]
                    ^^
```
Warning: subworkflows/local/amp.nf:111:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            input: [it[0], it[1]]
                           ^^
```
Warning: subworkflows/local/amp.nf:112:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            faa: it[2]
                 ^^
```
Warning: subworkflows/local/amp.nf:113:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            gbk: it[3]
                 ^^
```
Warning: subworkflows/local/amp.nf:114:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            interpro: it[4]
                      ^^
```

Warning: subworkflows/local/amp.nf:129:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_ampcombi_summaries = AMPCOMBI2_PARSETABLES.out.tsv.map { it[1] }.collect()
                                                                ^^

Warning: subworkflows/local/amp.nf:132:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_summary_count = ch_ampcombi_summaries.map { it.size() }.sum()
                                                   ^^

Warning: subworkflows/local/amp.nf:157:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_mmseqs_taxonomy_list = tsvs.map { it[1] }.collect()
                                             ^^
```

Warning: subworkflows/local/annotation.nf:65:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = PROKKA.out.txt.collect { it[1] }.ifEmpty([])
                                                    ^^

Warning: subworkflows/local/annotation.nf:85:28: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_bakta_hmm = Channel.fromPath(params.annotation_bakta_hmms, checkIfExists: true).first()
                           ^^^^^^^

Warning: subworkflows/local/annotation.nf:100:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = BAKTA_BAKTA.out.txt.collect { it[1] }.ifEmpty([])
                                                         ^^

Warning: subworkflows/local/arg.nf:60:94: Parameter was not used -- prefix with _ to suppress warning

            ch_input_to_argnorm_amrfinderplus = HAMRONIZATION_AMRFINDERPLUS.out.tsv.filter { meta, file -> !file.isEmpty() }
                                                                                             ^^^^

Warning: subworkflows/local/arg.nf:78:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                fastas: [it[0], it[1]]
                         ^^
```
Warning: subworkflows/local/arg.nf:78:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                fastas: [it[0], it[1]]
                                ^^
```
Warning: subworkflows/local/arg.nf:79:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                hmmclass: it[2]
                          ^^
```
Warning: subworkflows/local/arg.nf:100:49: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            rgi_db = UNTAR_CARD.out.untar.map { it[1] }
                                                ^^
```

Warning: subworkflows/local/arg.nf:164:82: Parameter was not used -- prefix with _ to suppress warning

            ch_input_to_argnorm_deeparg = HAMRONIZATION_DEEPARG.out.tsv.filter { meta, file -> !file.isEmpty() }
                                                                                 ^^^^

Warning: subworkflows/local/arg.nf:181:84: Parameter was not used -- prefix with _ to suppress warning

            ch_input_to_argnorm_abricate = HAMRONIZATION_ABRICATE.out.tsv.filter { meta, file -> !file.isEmpty() }
                                                                                   ^^^^

Warning: subworkflows/local/arg.nf:189:13: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it[1]
            ^^
```
Warning: subworkflows/local/arg.nf:200:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_mmseqs_taxonomy_list = tsvs.map { it[1] }.collect()
                                             ^^
```
Warning: subworkflows/local/bgc.nf:94:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                fastas: [it[0], it[1], []]
                         ^^
```
Warning: subworkflows/local/bgc.nf:94:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                fastas: [it[0], it[1], []]
                                ^^
```

Warning: subworkflows/local/bgc.nf:164:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_combgc_summaries = COMBGC.out.tsv.map { it[1] }.collectFile(name: 'combgc_complete_summary.tsv', storeDir: "${params.outdir}/reports/combgc", keepHeader: true)
                                                   ^^

Warning: subworkflows/local/bgc.nf:167:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_combgc_summaries = COMBGC.out.tsv.map { it[1] }.collectFile(name: 'combgc_complete_summary.tsv', keepHeader: true)
                                                   ^^

Warning: subworkflows/local/bgc.nf:173:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_mmseqs_taxonomy_list = tsvs.map { it[1] }.collect()
                                             ^^
```
Warning: subworkflows/local/taxa_class.nf:17:5: Variable was declared but not used
```
    ch_taxonomy_querydb = channel.empty()
    ^^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf:31:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf:102:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: workflows/funcscan.nf:74:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            compressed: it[1].toString().endsWith('.gz')
                        ^^
```
Warning: workflows/funcscan.nf:75:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            uncompressed: it[1]
                          ^^
```

Warning: workflows/funcscan.nf:87:44: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def fasta_found = files.find { it.toString().tokenize('.').last().matches('fasta|fas|fna|fa') }
                                           ^^

Warning: workflows/funcscan.nf:88:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def faa_found = files.find { it.toString().endsWith('.faa') }
                                         ^^

Warning: workflows/funcscan.nf:89:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def gbk_found = files.find { it.toString().tokenize('.').last().matches('gbk|gbff') }
                                         ^^

Warning: workflows/funcscan.nf:96:19: Parameter was not used -- prefix with _ to suppress warning
```
        .branch { meta, fasta, faa, gbk ->
                  ^^^^
```

Warning: workflows/funcscan.nf:96:25: Parameter was not used -- prefix with _ to suppress warning

        .branch { meta, fasta, faa, gbk ->
                        ^^^^^

Warning: workflows/funcscan.nf:96:32: Parameter was not used -- prefix with _ to suppress warning

        .branch { meta, fasta, faa, gbk ->
                               ^^^

Warning: workflows/funcscan.nf:104:75: Parameter was not used -- prefix with _ to suppress warning

        SEQKIT_SEQ_LENGTH(ch_intermediate_input.fastas.map { meta, fasta, faa, gbk -> [meta, fasta] })
                                                                          ^^^

Warning: workflows/funcscan.nf:104:80: Parameter was not used -- prefix with _ to suppress warning

        SEQKIT_SEQ_LENGTH(ch_intermediate_input.fastas.map { meta, fasta, faa, gbk -> [meta, fasta] })
                                                                               ^^^

Warning: workflows/funcscan.nf:106:33: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, fasta, protein, gbk -> [meta, fasta] }
                                ^^^^^^^

Warning: workflows/funcscan.nf:106:42: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, fasta, protein, gbk -> [meta, fasta] }
                                         ^^^

Warning: workflows/funcscan.nf:117:83: Parameter was not used -- prefix with _ to suppress warning

        ch_input_for_annotation = ch_intermediate_input.fastas.map { meta, fasta, protein, gbk -> [meta, fasta] }
                                                                                  ^^^^^^^

Warning: workflows/funcscan.nf:117:92: Parameter was not used -- prefix with _ to suppress warning

        ch_input_for_annotation = ch_intermediate_input.fastas.map { meta, fasta, protein, gbk -> [meta, fasta] }
                                                                                           ^^^

Warning: workflows/funcscan.nf:139:25: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, fasta, faa, gbk -> meta.category != 'long' }
                        ^^^^^

Warning: workflows/funcscan.nf:139:32: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, fasta, faa, gbk -> meta.category != 'long' }
                               ^^^

Warning: workflows/funcscan.nf:139:37: Parameter was not used -- prefix with _ to suppress warning

        .filter { meta, fasta, faa, gbk -> meta.category != 'long' }
                                    ^^^

Warning: workflows/funcscan.nf:150:29: Parameter was not used -- prefix with _ to suppress warning

            .filter { meta, fasta, faa, gbk -> meta.category == 'long' }
                            ^^^^^

Warning: workflows/funcscan.nf:150:36: Parameter was not used -- prefix with _ to suppress warning

            .filter { meta, fasta, faa, gbk -> meta.category == 'long' }
                                   ^^^

Warning: workflows/funcscan.nf:150:41: Parameter was not used -- prefix with _ to suppress warning

            .filter { meta, fasta, faa, gbk -> meta.category == 'long' }
                                        ^^^

Warning: workflows/funcscan.nf:173:9: Variable was declared but not used
```
        ch_mmseqs_db = channel.empty()
        ^^^^^^^^^^^^
```

Warning: workflows/funcscan.nf:174:9: Variable was declared but not used

        ch_taxonomy_querydb = channel.empty()
        ^^^^^^^^^^^^^^^^^^^

Warning: workflows/funcscan.nf:175:9: Variable was declared but not used

        ch_taxonomy_querydb_taxdb = channel.empty()
        ^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/funcscan.nf:431:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ANNOTATION.out.multiqc_files.collect { it[1] })
                                                                                       ^^

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