Nextflow lint results

Generated: 2026-03-17T00:28:36.851643963Z
Nextflow version: 26.02.0-edge
Summary: 96 warnings

⚠️ Warnings

Warning: conf/modules.config:94:273: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                ^^

Warning: conf/modules.config:127:273: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                ^^

Warning: conf/modules.config:155:273: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                ^^

Warning: conf/modules.config:185:308: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                                                   ^^

Warning: conf/modules.config:236:273: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                ^^

Warning: conf/modules.config:260:304: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                                               ^^

Warning: conf/modules.config:289:304: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                                               ^^

Warning: conf/modules.config:318:266: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                         ^^

Warning: conf/modules.config:347:266: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                         ^^

Warning: conf/modules.config:376:238: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                             ^^

Warning: conf/modules.config:404:238: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                             ^^

Warning: conf/modules.config:447:195: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && params.perform_shortread_hostremoval && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                  ^^

Warning: conf/modules.config:507:194: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && params.perform_longread_hostremoval && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                 ^^

Warning: conf/modules.config:569:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { !params.bracken_save_intermediatekraken2 && meta.tool == "bracken" ? null : it },
                                                                                                  ^^

Warning: modules/nf-core/bbmap/bbduk/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bracken/bracken/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/bracken/combinebrackenoutputs/main.nf:39:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

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

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

Warning: modules/nf-core/cat/fastq/main.nf:58:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: modules/nf-core/ganon/classify/main.nf:48:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/ganon/classify/main.nf:50:9: Variable was declared but not used

    def input = meta.single_end ? "--single-reads ${fastqs}" : "--paired-reads ${fastqs}"
        ^^^^^

Warning: modules/nf-core/ganon/report/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ganon/table/main.nf:36:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/kaiju/kaiju/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/kaiju/kaiju/main.nf:45:9: Variable was declared but not used

    def input = meta.single_end ? "-i ${reads}" : "-i ${reads[0]} -j ${reads[1]}"
        ^^^^^

Warning: modules/nf-core/kaiju/kaiju2krona/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/kaiju/kaiju2table/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/kmcp/profile/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/kmcp/search/main.nf:24:9: Variable was declared but not used

    def input  = meta.single_end ? "${reads}": "-1 ${reads[0]} -2 ${reads[1]}"
        ^^^^^

Warning: modules/nf-core/kmcp/search/main.nf:40:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/kraken2/kraken2/main.nf:60:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/kraken2/kraken2/main.nf:62:9: Variable was declared but not used

    def paired       = meta.single_end ? "" : "--paired"
        ^^^^^^

Warning: modules/nf-core/kraken2/kraken2/main.nf:65:9: Variable was declared but not used

    def readclassification_option = save_reads_assignment ? "--output ${prefix}.kraken2.classifiedreads.txt" : "--output /dev/null"
        ^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: modules/nf-core/kraken2/kraken2/main.nf:66:9: Variable was declared but not used

    def compress_reads_command = save_output_fastqs ? "pigz -p $task.cpus *.fastq" : ""
        ^^^^^^^^^^^^^^^^^^^^^^

Warning: modules/nf-core/krakentools/combinekreports/main.nf:36:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/krakentools/kreport2krona/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/malt/run/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/megan/rma2info/main.nf:40:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/megan/rma2info/main.nf:42:9: Variable was declared but not used

    def summary = megan_summary ? "-es ${prefix}.megan" : ""
        ^^^^^^^

Warning: modules/nf-core/melon/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/metaphlan/mergemetaphlantables/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/metaphlan/metaphlan/main.nf:58:9: Variable was declared but not used

    def input_data = ("${input_type}".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "${input}"
        ^^^^^^^^^^

Warning: modules/nf-core/metaphlan/metaphlan/main.nf:59:9: Variable was declared but not used

    def bowtie2_out = "${input_type}" == "--input_type bowtie2out" || "${input_type}" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
        ^^^^^^^^^^^

Warning: modules/nf-core/metaphlan/metaphlan/main.nf:60:9: Variable was declared but not used

    def samfile_out = save_samfile ? "-s ${prefix}.sam" : ''
        ^^^^^^^^^^^

Warning: modules/nf-core/minimap2/align/main.nf:67:9: Variable was declared but not used

    def target = reference ?: (bam_input ? error("BAM input requires reference") : reads)
        ^^^^^^

Warning: modules/nf-core/motus/merge/main.nf:47:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/motus/merge/main.nf:49:9: Variable was declared but not used

    def cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}"
        ^^^^^^^^^

Warning: modules/nf-core/motus/merge/main.nf:50:9: Variable was declared but not used

    def suffix = task.ext.args?.contains("-B") ? "biom" : "txt"
        ^^^^^^

Warning: modules/nf-core/motus/preplong/main.nf:49:9: Variable was declared but not used
```
    def refdb = db ? "-db ${db}" : ""
        ^^^^^
```
Warning: modules/nf-core/motus/profile/main.nf:58:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/motus/profile/main.nf:60:9: Variable was declared but not used
```
    def inputs = reads[0].getExtension() == 'bam' ?
        ^^^^^^
```
Warning: modules/nf-core/motus/profile/main.nf:65:9: Variable was declared but not used
```
    def refdb = db ? "-db ${db}" : ""
        ^^^^^
```
Warning: modules/nf-core/nanoq/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/nonpareil/curve/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/nonpareil/nonpareil/main.nf:46:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/nonpareil/nonpareilcurvesr/main.nf:44:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/nonpareil/set/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/porechop/abi/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/porechop/abi/main.nf:44:9: Variable was declared but not used

    def adapters_list = custom_adapters ? "--custom_adapters ${custom_adapters}" : ""
        ^^^^^^^^^^^^^

Warning: modules/nf-core/sylph/profile/main.nf:40:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/sylph/profile/main.nf:42:9: Variable was declared but not used

    def input = meta.single_end ? "${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
        ^^^^^

Warning: modules/nf-core/sylphtax/merge/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/taxpasta/merge/main.nf:46:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/taxpasta/merge/main.nf:48:9: Variable was declared but not used

    def taxonomy_option = taxonomy ? "--taxonomy ${taxonomy}" : ''
        ^^^^^^^^^^^^^^^

Warning: modules/nf-core/taxpasta/merge/main.nf:49:9: Variable was declared but not used

    def samplesheet_input = samplesheet ? "-s ${samplesheet}" : ''
        ^^^^^^^^^^^^^^^^^

Warning: modules/nf-core/taxpasta/standardise/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/taxpasta/standardise/main.nf:44:9: Variable was declared but not used

    def taxonomy_option = taxonomy ? "--taxonomy ${taxonomy}" : ''
        ^^^^^^^^^^^^^^^

Warning: subworkflows/local/profiling.nf:243:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                if (it[0].is_fasta) {
                    ^^
```

Warning: subworkflows/local/profiling.nf:244:145: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    log.warn("[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample ${it[0].id}.")
                                                                                                                                                ^^

Warning: subworkflows/local/profiling.nf:246:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                !it[0].is_fasta
                 ^^
```
Warning: subworkflows/local/profiling.nf:331:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                if (it[0].is_fasta) {
                    ^^
```

Warning: subworkflows/local/profiling.nf:332:135: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    log.warn("[nf-core/taxprofiler] mOTUs currently does not accept FASTA files as input. Skipping mOTUs for sample ${it[0].id}.")
                                                                                                                                      ^^

Warning: subworkflows/local/profiling.nf:334:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                !it[0].is_fasta
                 ^^
```

Warning: subworkflows/local/profiling.nf:337:27: Implicit closure parameter is deprecated, declare an explicit parameter instead

                longread: it[0].instrument_platform == 'OXFORD_NANOPORE' || it[0].instrument_platform == 'PACBIO_SMRT'
                          ^^

Warning: subworkflows/local/profiling.nf:337:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

                longread: it[0].instrument_platform == 'OXFORD_NANOPORE' || it[0].instrument_platform == 'PACBIO_SMRT'
                                                                            ^^

Warning: subworkflows/local/profiling.nf:338:28: Implicit closure parameter is deprecated, declare an explicit parameter instead

                shortread: it[0].instrument_platform != 'OXFORD_NANOPORE' && it[0].instrument_platform != 'PACBIO_SMRT'
                           ^^

Warning: subworkflows/local/profiling.nf:338:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

                shortread: it[0].instrument_platform != 'OXFORD_NANOPORE' && it[0].instrument_platform != 'PACBIO_SMRT'
                                                                             ^^

Warning: subworkflows/local/profiling.nf:530:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                if (it[0].is_fasta) {
                    ^^
```

Warning: subworkflows/local/profiling.nf:531:135: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    log.warn("[nf-core/taxprofiler] sylph currently does not accept FASTA files as input. Skipping sylph for sample ${it[0].id}.")
                                                                                                                                      ^^

Warning: subworkflows/local/profiling.nf:533:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                !it[0].is_fasta
                 ^^
```
Warning: subworkflows/local/shortread_adapterremoval.nf:19:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        single: it[0].single_end
                ^^
```
Warning: subworkflows/local/shortread_adapterremoval.nf:20:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        paired: !it[0].single_end
                 ^^
```
Warning: subworkflows/local/shortread_fastp.nf:18:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        single: it[0]['single_end'] == true
                ^^
```
Warning: subworkflows/local/shortread_fastp.nf:19:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        paired: it[0]['single_end'] == false
                ^^
```
Warning: subworkflows/local/visualization_krona.nf:28:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        centrifuge: it[0]['tool'] == 'centrifuge'
                    ^^
```
Warning: subworkflows/local/visualization_krona.nf:29:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        kraken2: it[0]['tool'] == 'kraken2' || it[0]['tool'] == 'kraken2-bracken'
                 ^^
```

Warning: subworkflows/local/visualization_krona.nf:29:48: Implicit closure parameter is deprecated, declare an explicit parameter instead

        kraken2: it[0]['tool'] == 'kraken2' || it[0]['tool'] == 'kraken2-bracken'
                                               ^^

Warning: subworkflows/local/visualization_krona.nf:33:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        kaiju: it[0]['tool'] == 'kaiju'
               ^^
```
Warning: subworkflows/local/visualization_krona.nf:34:15: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        malt: it[0]['tool'] == 'malt'
              ^^
```
Warning: subworkflows/local/visualization_krona.nf:79:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it[0]['db_name'], tool: it[0]['tool']], it[1]] }
                     ^^
```
Warning: subworkflows/local/visualization_krona.nf:79:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it[0]['db_name'], tool: it[0]['tool']], it[1]] }
                                             ^^
```

Warning: subworkflows/local/visualization_krona.nf:79:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [[id: it[0]['db_name'], tool: it[0]['tool']], it[1]] }
                                                             ^^

Warning: subworkflows/local/visualization_krona.nf:93:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [[id: it[0]['db_name'], tool: it[0]['tool']], it[1]] }
                         ^^
```

Warning: subworkflows/local/visualization_krona.nf:93:50: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [[id: it[0]['db_name'], tool: it[0]['tool']], it[1]] }
                                                 ^^

Warning: subworkflows/local/visualization_krona.nf:93:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [[id: it[0]['db_name'], tool: it[0]['tool']], it[1]] }
                                                                 ^^

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