Nextflow lint results

Generated: 2026-02-14T00:20:48.077453092Z
Nextflow version: 26.01.1-edge
Summary: 16 errors, 437 warnings

❌ Errors

Error: modules/local/initial_classification/main.nf:16:26: DOMAIN is not defined

    tuple val(meta), env(DOMAIN)                     , emit: domain
                         ^^^^^^

Error: modules/local/picard_format/main.nf:79:9: prefix is already declared

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

Error: modules/local/pick_assemblies/main.nf:20:26: COUNT is not defined

    tuple val(meta), env(COUNT)                     , emit: line_count
                         ^^^^^

Error: modules/local/vcf_to_snp_align/main.nf:17:30: SEQ_COUNT is not defined

    tuple val(ref_meta), env(SEQ_COUNT)                , emit: seq_count
                             ^^^^^^^^^

Error: modules/nf-core/sratools/fasterqdump/main.nf:58:9: prefix is already declared

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

Error: subworkflows/local/core_genome_phylogeny/main.nf:82:13: UNTAR is not defined
```
            UNTAR( bakta_db_tar )
            ^^^^^
```

Error: subworkflows/local/core_genome_phylogeny/main.nf:83:24: UNTAR is not defined

            bakta_db = UNTAR.out.untar.map{ meta, db -> db }.first()
                       ^^^^^

Error: subworkflows/local/core_genome_phylogeny/main.nf:84:37: UNTAR is not defined

            versions = versions.mix(UNTAR.out.versions)
                                    ^^^^^

Error: subworkflows/local/genome_assembly/main.nf:106:28: sample_data is already declared

        .map{ sample_meta, sample_data, paths ->
                           ^^^^^^^^^^^

Error: subworkflows/local/prepare_input/main.nf:333:53: read_count is already declared

            .map { sample_meta, fastq_paths, depth, read_count ->
                                                    ^^^^^^^^^^

Error: subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf:101:5: for loops are no longer supported
```
    for (param in checkPathParamList) {
    ^^^
```
Error: subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf:101:10: param is not defined
```
    for (param in checkPathParamList) {
         ^^^^^
```
Error: subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf:102:12: param is not defined
```
        if (param) { file(param, checkIfExists: true) }
           ^^^^^^^
```
Error: subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf:102:27: param is not defined
```
        if (param) { file(param, checkIfExists: true) }
                          ^^^^^
```

Error: workflows/pathogensurveillance.nf:181:28: versions is already declared

        .map {report_meta, versions, fastqc, fastp, nanoplot, quast ->
                           ^^^^^^^^

Error: workflows/pathogensurveillance.nf:182:13: Variables in a closure should be declared with def

            files = (fastqc ?: []) + (fastp ?: []) + (nanoplot ?: []) + (quast ?: []) + ([versions])
            ^^^^^

⚠️ Warnings

Warning: modules/local/assign_context_references/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/assign_mapping_reference/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/calculate_pocp/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/graphtyper/genotype/main.nf:26:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/graphtyper/genotype/main.nf:28:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def bai_path_text = bam.collect{"${it}.csi"}.join('\\n')
                                       ^^
```
Warning: modules/local/initial_classification/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/pick_assemblies/main.nf:27:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/prepare_report_input/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/vcf_to_snp_align/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/busco/download/main.nf:22:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${lineage}"
        ^^^^^^
```
Warning: modules/nf-core/busco/download/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/graphtyper/genotype/main.nf:26:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/graphtyper/genotype/main.nf:27:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def bam_path_text = bam.sort{it.name}.join('\\n')
                                 ^^
```
Warning: modules/nf-core/graphtyper/genotype/main.nf:28:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def index_path_text = index.sort{it.name}.join('\\n')
                                     ^^
```

Warning: modules/nf-core/graphtyper/vcfconcatenate/main.nf:27:44: Implicit closure parameter is deprecated, declare an explicit parameter instead

    input_vcfs = vcf.collate(1000).collect{it.join(' ')} // Batching needed because if there are too many VCFs the shell cannot run the command
                                           ^^

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

    def trees_rf_arg                = trees_rf                ? "-rf $trees_rf"                 : ''
        ^^^^^^^^^^^^

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

    def args      = task.ext.args   ?: ''
        ^^^^

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

    def features  = gff             ? "--features $gff" : ''
        ^^^^^^^^

Warning: modules/nf-core/quast/main.nf:51:9: Variable was declared but not used

    def reference = fasta           ? "-r $fasta" : ''
        ^^^^^^^^^

Warning: modules/nf-core/sourmash/compare/main.nf:32:48: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def sigs = signatures ? "${signatures.sort{it.toString()}.join(' ')}" : ''
                                               ^^

Warning: subworkflows/local/align_reads/main.nf:22:31: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                              ^^^^

Warning: subworkflows/local/align_reads/main.nf:22:45: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                            ^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:22:55: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                      ^^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:22:66: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                 ^^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:22:77: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                            ^^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:27:56: Parameter was not used -- prefix with _ to suppress warning

    ch_bwa_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                       ^^^^

Warning: subworkflows/local/align_reads/main.nf:27:62: Parameter was not used -- prefix with _ to suppress warning

    ch_bwa_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                             ^^^^^^

Warning: subworkflows/local/align_reads/main.nf:27:70: Parameter was not used -- prefix with _ to suppress warning

    ch_bwa_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                     ^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:27:80: Parameter was not used -- prefix with _ to suppress warning

    ch_bwa_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                               ^^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:27:91: Parameter was not used -- prefix with _ to suppress warning

    ch_bwa_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                                          ^^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:34:56: Parameter was not used -- prefix with _ to suppress warning

    ch_reference = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                       ^^^^

Warning: subworkflows/local/align_reads/main.nf:34:62: Parameter was not used -- prefix with _ to suppress warning

    ch_reference = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                             ^^^^^^

Warning: subworkflows/local/align_reads/main.nf:34:70: Parameter was not used -- prefix with _ to suppress warning

    ch_reference = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                     ^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:34:91: Parameter was not used -- prefix with _ to suppress warning

    ch_reference = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                                          ^^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:34:102: Parameter was not used -- prefix with _ to suppress warning

    ch_reference = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                                                     ^^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:37:56: Parameter was not used -- prefix with _ to suppress warning

    ch_ref_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                       ^^^^

Warning: subworkflows/local/align_reads/main.nf:37:62: Parameter was not used -- prefix with _ to suppress warning

    ch_ref_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                             ^^^^^^

Warning: subworkflows/local/align_reads/main.nf:37:70: Parameter was not used -- prefix with _ to suppress warning

    ch_ref_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                     ^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:37:80: Parameter was not used -- prefix with _ to suppress warning

    ch_ref_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                               ^^^^^^^^^

Warning: subworkflows/local/align_reads/main.nf:37:102: Parameter was not used -- prefix with _ to suppress warning

    ch_ref_index = samp_ref_combo.map { combined_meta, meta, fastqs, ref_meta, reference, ref_index, bam_index ->
                                                                                                     ^^^^^^^^^

Warning: subworkflows/local/busco_phylogeny/main.nf:22:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{it.domain == "Eukaryota"}
                ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:26:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
               ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:26:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
                             ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:26:51: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
                                                  ^^
```

Warning: subworkflows/local/busco_phylogeny/main.nf:32:82: Parameter was not used -- prefix with _ to suppress warning

        .collectFile() { sample_id, report_group_id, ref_id, ref_name, ref_desc, ref_path, usage ->
                                                                                 ^^^^^^^^

Warning: subworkflows/local/busco_phylogeny/main.nf:35:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName()], it]}
                    ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:35:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName()], it]}
                                         ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:48:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.report_group_ids], it.ref_metas] }
                    ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:48:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.report_group_ids], it.ref_metas] }
                                          ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:57:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[0], it[1].replace('\n', '')] } // remove newline that splitText adds
                ^^
```

Warning: subworkflows/local/busco_phylogeny/main.nf:57:24: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it[0], it[1].replace('\n', '')] } // remove newline that splitText adds
                       ^^

Warning: subworkflows/local/busco_phylogeny/main.nf:63:48: Parameter was not used -- prefix with _ to suppress warning

        .map {report_meta, ref_meta, ref_path, ref_name ->
                                               ^^^^^^^^

Warning: subworkflows/local/busco_phylogeny/main.nf:69:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:69:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```

Warning: subworkflows/local/busco_phylogeny/main.nf:80:25: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, report_meta, path ->
                        ^^^^^^^^^^^

Warning: subworkflows/local/busco_phylogeny/main.nf:95:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ meta, report_meta, path, busco_dir ->
              ^^^^
```

Warning: subworkflows/local/busco_phylogeny/main.nf:95:34: Parameter was not used -- prefix with _ to suppress warning

        .map{ meta, report_meta, path, busco_dir ->
                                 ^^^^

Warning: subworkflows/local/busco_phylogeny/main.nf:110:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.sample_id == '' ? null : [id: it.sample_id],
                ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:110:50: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.sample_id == '' ? null : [id: it.sample_id],
                                                 ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:111:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.report_group_id == '' ? null : [id: it.report_group_id],
                ^^
```

Warning: subworkflows/local/busco_phylogeny/main.nf:111:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it.report_group_id == '' ? null : [id: it.report_group_id],
                                                       ^^

Warning: subworkflows/local/busco_phylogeny/main.nf:112:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.reference_id == '' ? null : [id: it.reference_id],
                ^^
```

Warning: subworkflows/local/busco_phylogeny/main.nf:112:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it.reference_id == '' ? null : [id: it.reference_id],
                                                    ^^

Warning: subworkflows/local/busco_phylogeny/main.nf:114:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.message_type,
                ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:115:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.description
                ^^
```
Warning: subworkflows/local/busco_phylogeny/main.nf:140:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[0].group_id, it[1]] } // group_meta, tree
                ^^
```

Warning: subworkflows/local/busco_phylogeny/main.nf:140:33: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it[0].group_id, it[1]] } // group_meta, tree
                                ^^

Warning: subworkflows/local/call_variants/main.nf:29:30: Parameter was not used -- prefix with _ to suppress warning

        .map{ combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                             ^^^^^^^^^^^

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

        .map{ combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                          ^^^

Warning: subworkflows/local/call_variants/main.nf:29:48: Parameter was not used -- prefix with _ to suppress warning

        .map{ combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                               ^^^

Warning: subworkflows/local/call_variants/main.nf:29:53: Parameter was not used -- prefix with _ to suppress warning

        .map{ combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                                    ^^^

Warning: subworkflows/local/call_variants/main.nf:29:58: Parameter was not used -- prefix with _ to suppress warning

        .map{ combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                                         ^^^

Warning: subworkflows/local/call_variants/main.nf:29:63: Parameter was not used -- prefix with _ to suppress warning

        .map{ combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                                              ^^^^

Warning: subworkflows/local/call_variants/main.nf:34:31: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                              ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:34:44: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                           ^^^

Warning: subworkflows/local/call_variants/main.nf:34:49: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:34:59: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                                          ^^^

Warning: subworkflows/local/call_variants/main.nf:34:64: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict ->
                                                               ^^^^

Warning: subworkflows/local/call_variants/main.nf:41:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it.getSimpleName(), it] }
                ^^
```
Warning: subworkflows/local/call_variants/main.nf:41:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it.getSimpleName(), it] }
                                    ^^
```

Warning: subworkflows/local/call_variants/main.nf:43:16: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta_id, region_path, combined_meta ->
               ^^^^^^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:50:45: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                            ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:50:68: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                   ^^^

Warning: subworkflows/local/call_variants/main.nf:50:73: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                        ^^^

Warning: subworkflows/local/call_variants/main.nf:50:78: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                             ^^^^

Warning: subworkflows/local/call_variants/main.nf:50:84: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                                   ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:53:45: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                            ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:53:58: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                         ^^^

Warning: subworkflows/local/call_variants/main.nf:53:63: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                              ^^^

Warning: subworkflows/local/call_variants/main.nf:53:73: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                        ^^^

Warning: subworkflows/local/call_variants/main.nf:53:78: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                             ^^^^

Warning: subworkflows/local/call_variants/main.nf:53:84: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                                   ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:56:45: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                            ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:56:58: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                         ^^^

Warning: subworkflows/local/call_variants/main.nf:56:63: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                              ^^^

Warning: subworkflows/local/call_variants/main.nf:56:68: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                   ^^^

Warning: subworkflows/local/call_variants/main.nf:56:78: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                             ^^^^

Warning: subworkflows/local/call_variants/main.nf:56:84: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                                   ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:59:30: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                             ^^^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:59:45: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                            ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:59:58: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                         ^^^

Warning: subworkflows/local/call_variants/main.nf:59:63: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                              ^^^

Warning: subworkflows/local/call_variants/main.nf:59:68: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                   ^^^

Warning: subworkflows/local/call_variants/main.nf:59:73: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                        ^^^

Warning: subworkflows/local/call_variants/main.nf:59:78: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                             ^^^^

Warning: subworkflows/local/call_variants/main.nf:74:45: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                            ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:74:58: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                         ^^^

Warning: subworkflows/local/call_variants/main.nf:74:63: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                              ^^^

Warning: subworkflows/local/call_variants/main.nf:74:73: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                        ^^^

Warning: subworkflows/local/call_variants/main.nf:74:78: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                             ^^^^

Warning: subworkflows/local/call_variants/main.nf:74:84: Parameter was not used -- prefix with _ to suppress warning

        ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                                   ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:84:49: Parameter was not used -- prefix with _ to suppress warning

            ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:84:62: Parameter was not used -- prefix with _ to suppress warning

            ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                             ^^^

Warning: subworkflows/local/call_variants/main.nf:84:67: Parameter was not used -- prefix with _ to suppress warning

            ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                  ^^^

Warning: subworkflows/local/call_variants/main.nf:84:88: Parameter was not used -- prefix with _ to suppress warning

            ch_ref_grouped.map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                                       ^^^^^^^^^^^

Warning: subworkflows/local/call_variants/main.nf:90:49: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:90:54: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                     ^^^

Warning: subworkflows/local/call_variants/main.nf:90:59: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                          ^^^^

Warning: subworkflows/local/call_variants/main.nf:90:65: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:93:39: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                      ^^^

Warning: subworkflows/local/call_variants/main.nf:93:44: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                           ^^^

Warning: subworkflows/local/call_variants/main.nf:93:54: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                     ^^^

Warning: subworkflows/local/call_variants/main.nf:93:59: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                          ^^^^

Warning: subworkflows/local/call_variants/main.nf:93:65: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:96:39: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                      ^^^

Warning: subworkflows/local/call_variants/main.nf:96:44: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                           ^^^

Warning: subworkflows/local/call_variants/main.nf:96:49: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:96:59: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                          ^^^^

Warning: subworkflows/local/call_variants/main.nf:96:65: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:99:39: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                      ^^^

Warning: subworkflows/local/call_variants/main.nf:99:44: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                           ^^^

Warning: subworkflows/local/call_variants/main.nf:99:49: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:99:54: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                     ^^^

Warning: subworkflows/local/call_variants/main.nf:99:65: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:102:39: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                      ^^^

Warning: subworkflows/local/call_variants/main.nf:102:44: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                           ^^^

Warning: subworkflows/local/call_variants/main.nf:102:49: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:102:54: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                     ^^^

Warning: subworkflows/local/call_variants/main.nf:102:59: Parameter was not used -- prefix with _ to suppress warning

        vf_input.map { combined_meta, vcf, tbi, ref, fai, dict, gzi ->
                                                          ^^^^

Warning: subworkflows/local/call_variants/main.nf:115:44: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                           ^^^

Warning: subworkflows/local/call_variants/main.nf:115:49: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                ^^^

Warning: subworkflows/local/call_variants/main.nf:115:54: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                     ^^^

Warning: subworkflows/local/call_variants/main.nf:115:59: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                          ^^^

Warning: subworkflows/local/call_variants/main.nf:115:64: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                               ^^^^

Warning: subworkflows/local/call_variants/main.nf:115:70: Parameter was not used -- prefix with _ to suppress warning

        .map { combined_meta, sample_meta, bam, bai, ref, fai, dict, region_file ->
                                                                     ^^^^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:27:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{it.domain == "Bacteria" || it.domain == "Archaea"}
                ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:27:44: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{it.domain == "Bacteria" || it.domain == "Archaea"}
                                           ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:31:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
               ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:31:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
                             ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:31:51: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
                                                  ^^
```

Warning: subworkflows/local/core_genome_phylogeny/main.nf:37:82: Parameter was not used -- prefix with _ to suppress warning

        .collectFile() { sample_id, report_group_id, ref_id, ref_name, ref_desc, ref_path, usage ->
                                                                                 ^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:40:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName()], it]}
                    ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:40:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName()], it]}
                                         ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:53:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.report_group_ids], it.ref_metas] }
                    ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:53:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.report_group_ids], it.ref_metas] }
                                          ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:63:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[0], it[1].replace('\n', '')] } // remove newline that splitText adds
                ^^
```

Warning: subworkflows/local/core_genome_phylogeny/main.nf:63:24: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it[0], it[1].replace('\n', '')] } // remove newline that splitText adds
                       ^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:72:19: Parameter was not used -- prefix with _ to suppress warning
```
        .branch { ref_meta, report_meta, ref_path, gff_path ->
                  ^^^^^^^^
```

Warning: subworkflows/local/core_genome_phylogeny/main.nf:72:29: Parameter was not used -- prefix with _ to suppress warning

        .branch { ref_meta, report_meta, ref_path, gff_path ->
                            ^^^^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:72:42: Parameter was not used -- prefix with _ to suppress warning

        .branch { ref_meta, report_meta, ref_path, gff_path ->
                                         ^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:81:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

            bakta_db_tar = channel.fromPath(params.bakta_db).map{ [ [id: 'baktadb'], it] }
                                                                                     ^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:83:45: Parameter was not used -- prefix with _ to suppress warning

            bakta_db = UNTAR.out.untar.map{ meta, db -> db }.first()
                                            ^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:96:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:96:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```

Warning: subworkflows/local/core_genome_phylogeny/main.nf:99:49: Parameter was not used -- prefix with _ to suppress warning

        .map { ref_meta, report_meta, ref_path, gff_path ->
                                                ^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:106:30: Parameter was not used -- prefix with _ to suppress warning

            .map { ref_meta, report_meta, assem_path ->
                             ^^^^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:121:29: Parameter was not used -- prefix with _ to suppress warning

            .map{ ref_meta, report_meta, ref_path, ref_gff ->
                            ^^^^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:130:49: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_or_ref_meta, report_meta, assem_path, gff_path ->
                                                ^^^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:135:38: Parameter was not used -- prefix with _ to suppress warning

        .map{ ref_meta, report_meta, ref_path, ref_gff, ref_combined ->
                                     ^^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:135:48: Parameter was not used -- prefix with _ to suppress warning

        .map{ ref_meta, report_meta, ref_path, ref_gff, ref_combined ->
                                               ^^^^^^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:140:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample_or_ref_meta, report_meta, gff ->
               ^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:152:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[1].any{ it.endsWith("PIRATE.gene_families.ordered.tsv") } }
                  ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:152:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[1].any{ it.endsWith("PIRATE.gene_families.ordered.tsv") } }
                             ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:154:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { ! it[1].any{ it.endsWith("PIRATE.gene_families.ordered.tsv") } }
                    ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:154:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { ! it[1].any{ it.endsWith("PIRATE.gene_families.ordered.tsv") } }
                               ^^
```

Warning: subworkflows/local/core_genome_phylogeny/main.nf:155:23: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [null, it[0], null, "CORE_GENOME_PHYLOGENY", "WARNING", "Pirate failed to find a core genome, possibly becuase samples are very different or there are too few reads."] } // meta, group_meta, ref_meta, workflow, level, message
                      ^^

Warning: subworkflows/local/core_genome_phylogeny/main.nf:184:20: Parameter was not used -- prefix with _ to suppress warning
```
            .map { file_name, message_data -> [
                   ^^^^^^^^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:215:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[0].group_id, it[1]] } // group_meta, tree
                ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:215:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[0].group_id, it[1]] } // group_meta, tree
                                ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:220:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[1], null] }
                ^^
```
Warning: subworkflows/local/core_genome_phylogeny/main.nf:223:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[1], null] }
                ^^
```

Warning: subworkflows/local/genome_assembly/main.nf:17:21: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [[id: it.sample_id, single_end: it.single_end, domain: it.domain, type: it.sequence_type], [id: it.report_group_ids], it.paths] }
                    ^^

Warning: subworkflows/local/genome_assembly/main.nf:17:47: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [[id: it.sample_id, single_end: it.single_end, domain: it.domain, type: it.sequence_type], [id: it.report_group_ids], it.paths] }
                                              ^^

Warning: subworkflows/local/genome_assembly/main.nf:17:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [[id: it.sample_id, single_end: it.single_end, domain: it.domain, type: it.sequence_type], [id: it.report_group_ids], it.paths] }
                                                                     ^^

Warning: subworkflows/local/genome_assembly/main.nf:17:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [[id: it.sample_id, single_end: it.single_end, domain: it.domain, type: it.sequence_type], [id: it.report_group_ids], it.paths] }
                                                                                      ^^

Warning: subworkflows/local/genome_assembly/main.nf:17:111: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [[id: it.sample_id, single_end: it.single_end, domain: it.domain, type: it.sequence_type], [id: it.report_group_ids], it.paths] }
                                                                                                              ^^

Warning: subworkflows/local/genome_assembly/main.nf:17:133: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [[id: it.sample_id, single_end: it.single_end, domain: it.domain, type: it.sequence_type], [id: it.report_group_ids], it.paths] }
                                                                                                                                    ^^

Warning: subworkflows/local/genome_assembly/main.nf:19:28: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, read_paths -> [sample_meta, read_paths]}
                           ^^^^^^^^^^^

Warning: subworkflows/local/genome_assembly/main.nf:21:25: Parameter was not used -- prefix with _ to suppress warning
```
        .branch { meta, paths->
                        ^^^^^
```

Warning: subworkflows/local/genome_assembly/main.nf:36:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [sample_meta, read_paths.size() <= 2 ? read_paths : read_paths.findAll { it ==~ /.+_[12]\..+$/ }, [] ]
                                                                                     ^^

Warning: subworkflows/local/genome_assembly/main.nf:43:18: Parameter was not used -- prefix with _ to suppress warning
```
        .filter{ sample_meta, json ->
                 ^^^^^^^^^^^
```

Warning: subworkflows/local/genome_assembly/main.nf:57:29: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, read_paths1, base_count, report_meta, read_paths2 ->
                            ^^^^^^^^^^^

Warning: subworkflows/local/genome_assembly/main.nf:57:67: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, read_paths1, base_count, report_meta, read_paths2 ->
                                                                  ^^^^^^^^^^^

Warning: subworkflows/local/genome_assembly/main.nf:72:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { sample_meta, read_paths, scaffolds ->
                  ^^^^^^^^^^^
```

Warning: subworkflows/local/genome_assembly/main.nf:72:32: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, read_paths, scaffolds ->
                               ^^^^^^^^^^

Warning: subworkflows/local/genome_assembly/main.nf:76:29: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, read_paths, scaffolds, report_meta, read_paths2 ->
                            ^^^^^^^^^^

Warning: subworkflows/local/genome_assembly/main.nf:76:41: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, read_paths, scaffolds, report_meta, read_paths2 ->
                                        ^^^^^^^^^

Warning: subworkflows/local/genome_assembly/main.nf:76:65: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, read_paths, scaffolds, report_meta, read_paths2 ->
                                                                ^^^^^^^^^^^

Warning: subworkflows/local/genome_assembly/main.nf:104:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it] }
                     ^^
```
Warning: subworkflows/local/genome_assembly/main.nf:104:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it] }
                                    ^^
```

Warning: subworkflows/local/genome_assembly/main.nf:106:41: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, sample_data, paths ->
                                        ^^^^^

Warning: subworkflows/local/initial_qc_checks/main.nf:15:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it.sequence_type == "illumina" || it.sequence_type == "bgiseq" }
                  ^^
```

Warning: subworkflows/local/initial_qc_checks/main.nf:15:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .filter { it.sequence_type == "illumina" || it.sequence_type == "bgiseq" }
                                                    ^^

Warning: subworkflows/local/initial_qc_checks/main.nf:16:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths] }
                     ^^
```
Warning: subworkflows/local/initial_qc_checks/main.nf:16:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths] }
                                    ^^
```
Warning: subworkflows/local/initial_qc_checks/main.nf:22:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it.sequence_type == "nanopore" || it.sequence_type == "pacbio" }
                  ^^
```

Warning: subworkflows/local/initial_qc_checks/main.nf:22:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .filter { it.sequence_type == "nanopore" || it.sequence_type == "pacbio" }
                                                    ^^

Warning: subworkflows/local/initial_qc_checks/main.nf:23:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths] }
                     ^^
```
Warning: subworkflows/local/initial_qc_checks/main.nf:23:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths] }
                                    ^^
```
Warning: subworkflows/local/prepare_input/main.nf:31:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_sample_metadata_channel(it) }
                                              ^^
```
Warning: subworkflows/local/prepare_input/main.nf:35:50: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_reference_metadata_channel(it) }
                                                 ^^
```
Warning: subworkflows/local/prepare_input/main.nf:41:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.sample_id == '' ? null : [id: it.sample_id],
                ^^
```

Warning: subworkflows/local/prepare_input/main.nf:41:50: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it.sample_id == '' ? null : [id: it.sample_id],
                                                 ^^

Warning: subworkflows/local/prepare_input/main.nf:42:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.report_group_id == '' ? null : [id: it.report_group_id],
                ^^
```

Warning: subworkflows/local/prepare_input/main.nf:42:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it.report_group_id == '' ? null : [id: it.report_group_id],
                                                       ^^

Warning: subworkflows/local/prepare_input/main.nf:43:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.reference_id == '' ? null : [id: it.reference_id],
                ^^
```

Warning: subworkflows/local/prepare_input/main.nf:43:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it.reference_id == '' ? null : [id: it.reference_id],
                                                    ^^

Warning: subworkflows/local/prepare_input/main.nf:45:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.message_type,
                ^^
```
Warning: subworkflows/local/prepare_input/main.nf:46:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it.description
                ^^
```
Warning: subworkflows/local/prepare_input/main.nf:56:27: Parameter was not used -- prefix with _ to suppress warning
```
        .filter{ ref_ids, sample_meta -> ref_ids.size() > 0 }
                          ^^^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:59:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { ref_id, sample_meta, ref_meta -> [sample_meta, ref_meta] }
               ^^^^^^
```

Warning: subworkflows/local/prepare_input/main.nf:65:31: Parameter was not used -- prefix with _ to suppress warning

        .filter{ sample_meta, ref_metas -> sample_meta.ncbi_accession}
                              ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:67:31: Parameter was not used -- prefix with _ to suppress warning

        .filter{ sample_meta, ref_metas -> ! sample_meta.ncbi_accession }
                              ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:72:31: Parameter was not used -- prefix with _ to suppress warning

        .map { ncbi_acc_meta, sample_meta, ref_metas ->
                              ^^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:72:44: Parameter was not used -- prefix with _ to suppress warning

        .map { ncbi_acc_meta, sample_meta, ref_metas ->
                                           ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:80:16: Parameter was not used -- prefix with _ to suppress warning

        .map { ncbi_acc_meta, reads_path, sample_meta, ref_metas ->
               ^^^^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:85:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    sample_meta.paths = reads_path.findAll{it ==~ /^.+_[12]\..+$/}
                                                           ^^

Warning: subworkflows/local/prepare_input/main.nf:98:33: Parameter was not used -- prefix with _ to suppress warning

            .map { sample_meta, ref_metas ->
                                ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:122:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ sample_id, sample_meta, ref_metas, depth, domain ->
              ^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:131:18: Parameter was not used -- prefix with _ to suppress warning
```
        .filter{ sample_meta, taxon_data ->
                 ^^^^^^^^^^^
```

Warning: subworkflows/local/prepare_input/main.nf:139:19: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, ref_metas -> // Dont lookup assembly metadata if no references are to be dowloaded automatically (besides user-defined references)
                  ^^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:139:32: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, ref_metas -> // Dont lookup assembly metadata if no references are to be dowloaded automatically (besides user-defined references)
                               ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:142:19: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, ref_metas -> // Dont lookup assembly metadata for samples that the user has defined exclusive references for
                  ^^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:143:34: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ! (ref_metas.collect{it.ref_primary_usage}.contains('exclusive') &&
                                 ^^

Warning: subworkflows/local/prepare_input/main.nf:144:36: Implicit closure parameter is deprecated, declare an explicit parameter instead

                (ref_metas.collect{it.ref_contextual_usage}.contains('exclusive') || no_auto_contextual_refs))
                                   ^^

Warning: subworkflows/local/prepare_input/main.nf:146:29: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, ref_metas ->
                            ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:150:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ sample_id, sample_meta, family_ids -> [family_ids] }
              ^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:150:26: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ sample_id, sample_meta, family_ids -> [family_ids] }
                         ^^^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:168:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample_meta, family_ids ->
               ^^^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:173:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it != [null, null] }
                  ^^
```
Warning: subworkflows/local/prepare_input/main.nf:179:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { family_id, sample_id, stats_path -> [sample_id, stats_path] }
               ^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:183:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            [sample_id, family_stats.findAll{it != null}]
                                             ^^
```

Warning: subworkflows/local/prepare_input/main.nf:186:29: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, ref_metas -> [[id: sample_meta.sample_id]] }
                            ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:190:19: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, taxa_found, family_stats ->
                  ^^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:190:32: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, taxa_found, family_stats ->
                               ^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:204:29: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, ref_metas -> [[id: sample_meta.sample_id]] }
                            ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:207:19: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .filter { it != [null, null] } // above join adds [null, null] if channel is empty
                  ^^

Warning: subworkflows/local/prepare_input/main.nf:216:29: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, ref_metas -> [[id: sample_meta.sample_id]] }
                            ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:219:19: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .filter { it != [null, null] } // above join adds [null, null] if channel is empty
                  ^^

Warning: subworkflows/local/prepare_input/main.nf:230:27: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_id, sample_meta, ref_metas_user, ref_metas_to_download ->
                          ^^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:233:48: Parameter was not used -- prefix with _ to suppress warning

        .combine(sample_data.map{ sample_meta, ref_metas -> [[id: sample_meta.sample_id], sample_meta] }, by: 0)
                                               ^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:234:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample_id, ref_metas, sample_meta ->
               ^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:240:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ sample_id, ref_meta -> ref_meta }
              ^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:245:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { sample_id, line_count ->
                  ^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:249:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample_id, line_count, sample_meta, ref_metas ->
               ^^^^^^^^^
```

Warning: subworkflows/local/prepare_input/main.nf:249:27: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_id, line_count, sample_meta, ref_metas ->
                          ^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:253:28: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ sample_meta, ref_metas ->
                           ^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:261:15: Variable was declared but not used
```
        .tap{ ref_data_with_ncbi_acc }
              ^^^^^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/prepare_input/main.nf:270:18: Parameter was not used -- prefix with _ to suppress warning
```
        .filter{ sample_meta, ref_meta ->
                 ^^^^^^^^^^^
```

Warning: subworkflows/local/prepare_input/main.nf:281:16: Parameter was not used -- prefix with _ to suppress warning

        .map { ncbi_acc_meta, sample_meta, ref_meta, ref_path, gff_path ->
               ^^^^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:306:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths, it.sendsketch_depth] }
                     ^^
```
Warning: subworkflows/local/prepare_input/main.nf:306:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths, it.sendsketch_depth] }
                                    ^^
```
Warning: subworkflows/local/prepare_input/main.nf:306:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths, it.sendsketch_depth] }
                                              ^^
```
Warning: subworkflows/local/prepare_input/main.nf:308:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { sample_id, fastq_paths, depth ->
                  ^^^^^^^^^
```

Warning: subworkflows/local/prepare_input/main.nf:308:30: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_id, fastq_paths, depth ->
                             ^^^^^^^^^^^

Warning: subworkflows/local/prepare_input/main.nf:313:13: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it.sendsketch_depth.toFloat() <= params.max_depth.toFloat()
            ^^
```

Warning: subworkflows/local/prepare_input/main.nf:317:46: Parameter was not used -- prefix with _ to suppress warning

            .map { sample_meta, fastq_paths, depth ->
                                             ^^^^^

Warning: subworkflows/local/prepare_input/main.nf:343:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample_id, sample_meta, subset_reads ->
               ^^^^^^^^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:17:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths] }
                     ^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:17:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], it.paths] }
                                    ^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:36:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.ref_metas] }
               ^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:48:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], [id: it.report_group_ids]] }
                     ^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:48:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], [id: it.report_group_ids]] }
                                         ^^
```

Warning: subworkflows/local/sketch_comparison/main.nf:50:16: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_id, report_group_id, signature -> [report_group_id, signature]}
               ^^^^^^^^^

Warning: subworkflows/local/sketch_comparison/main.nf:53:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.ref_metas, [id: it.report_group_ids]] }
               ^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:53:35: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.ref_metas, [id: it.report_group_ids]] }
                                  ^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:57:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ ref_id, report_group_id, signature -> [report_group_id, signature]}
              ^^^^^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:60:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], [id: it.report_group_ids]] }
                     ^^
```
Warning: subworkflows/local/sketch_comparison/main.nf:60:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: it.sample_id], [id: it.report_group_ids]] }
                                         ^^
```

Warning: subworkflows/local/sketch_comparison/main.nf:62:15: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_id, report_group_id, signature -> [report_group_id, signature]}
              ^^^^^^^^^

Warning: subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf:26:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf:29:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf:33:5: Parameter was not used -- prefix with _ to suppress warning
```
    reference_data    //  string: Path to reference data samplesheet
    ^^^^^^^^^^^^^^
```
Warning: subworkflows/local/variant_analysis/main.nf:21:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{[[id: it.report_group_ids], it]}
                   ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:21:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{[[id: it.report_group_ids], it]}
                                         ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:24:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it[1].size() > 1 }
                 ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:26:15: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ it[1] }
              ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:29:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[1].size() == 1 }
                     ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:37:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
               ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:37:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
                             ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:37:51: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [it.sample_id, it.report_group_ids, it.ref_metas] }
                                                  ^^
```

Warning: subworkflows/local/variant_analysis/main.nf:44:82: Parameter was not used -- prefix with _ to suppress warning

        .collectFile() { sample_id, report_group_id, ref_id, ref_name, ref_desc, ref_path, usage ->
                                                                                 ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:47:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName()], it]}
                    ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:47:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName()], it]}
                                         ^^
```

Warning: subworkflows/local/variant_analysis/main.nf:56:51: Parameter was not used -- prefix with _ to suppress warning

        .map {sample_id, report_group_id, ref_id, ref_name, ref_desc, ref_path, usage ->
                                                  ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:56:61: Parameter was not used -- prefix with _ to suppress warning

        .map {sample_id, report_group_id, ref_id, ref_name, ref_desc, ref_path, usage ->
                                                            ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:62:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it[0], it[1].replace('\n', '')] } // remove newline that splitText adds
                ^^
```

Warning: subworkflows/local/variant_analysis/main.nf:62:24: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [it[0], it[1].replace('\n', '')] } // remove newline that splitText adds
                       ^^

Warning: subworkflows/local/variant_analysis/main.nf:68:38: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .join(sample_data.map{ [[id: it.sample_id], [id: it.report_group_ids], it.paths, it.sequence_type, it.ploidy] }, by: 0..1)
                                     ^^

Warning: subworkflows/local/variant_analysis/main.nf:68:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .join(sample_data.map{ [[id: it.sample_id], [id: it.report_group_ids], it.paths, it.sequence_type, it.ploidy] }, by: 0..1)
                                                         ^^

Warning: subworkflows/local/variant_analysis/main.nf:68:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .join(sample_data.map{ [[id: it.sample_id], [id: it.report_group_ids], it.paths, it.sequence_type, it.ploidy] }, by: 0..1)
                                                                               ^^

Warning: subworkflows/local/variant_analysis/main.nf:68:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .join(sample_data.map{ [[id: it.sample_id], [id: it.report_group_ids], it.paths, it.sequence_type, it.ploidy] }, by: 0..1)
                                                                                         ^^

Warning: subworkflows/local/variant_analysis/main.nf:68:108: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .join(sample_data.map{ [[id: it.sample_id], [id: it.report_group_ids], it.paths, it.sequence_type, it.ploidy] }, by: 0..1)
                                                                                                           ^^

Warning: subworkflows/local/variant_analysis/main.nf:70:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            filtered: it[2] != null
                      ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:71:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_ref: it[2] == null
                    ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:81:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it[2].size() >= 2 }
                 ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:83:15: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ it[2] }
              ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:86:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter{ it[2].size() < 2 }
                     ^^
```

Warning: subworkflows/local/variant_analysis/main.nf:94:19: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                  ^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:94:32: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                               ^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:94:45: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                            ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:94:55: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                      ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:94:65: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                ^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:94:72: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                       ^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:94:99: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                                  ^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:98:38: Parameter was not used -- prefix with _ to suppress warning

        longreads.map { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                     ^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:98:51: Parameter was not used -- prefix with _ to suppress warning

        longreads.map { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                  ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:98:61: Parameter was not used -- prefix with _ to suppress warning

        longreads.map { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                            ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:98:71: Parameter was not used -- prefix with _ to suppress warning

        longreads.map { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                      ^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:98:90: Parameter was not used -- prefix with _ to suppress warning

        longreads.map { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                         ^^^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:98:105: Parameter was not used -- prefix with _ to suppress warning

        longreads.map { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                                        ^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:106:84: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, chopped_reads, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                   ^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:110:19: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                  ^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:110:32: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                               ^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:110:45: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                            ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:110:55: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                      ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:110:65: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                ^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:110:72: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                       ^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:110:99: Parameter was not used -- prefix with _ to suppress warning

        .filter { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                                  ^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:118:41: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                        ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:118:51: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                  ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:118:61: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                            ^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:118:68: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                   ^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:118:80: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                               ^^^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:118:95: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                              ^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:126:19: Parameter was not used -- prefix with _ to suppress warning

            .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                  ^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:126:32: Parameter was not used -- prefix with _ to suppress warning

            .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                               ^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:126:65: Parameter was not used -- prefix with _ to suppress warning

            .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                ^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:126:72: Parameter was not used -- prefix with _ to suppress warning

            .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                       ^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:126:84: Parameter was not used -- prefix with _ to suppress warning

            .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                   ^^^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:126:99: Parameter was not used -- prefix with _ to suppress warning

            .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                                  ^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:134:61: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                            ^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:134:80: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                               ^^^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:134:95: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                              ^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:146:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { it[0..3] + it[5..6] }
                   ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:146:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { it[0..3] + it[5..6] }
                              ^^
```

Warning: subworkflows/local/variant_analysis/main.nf:153:21: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [it[0], it[2], it[1]] + it[3..5] + [it[7]] } // [val(meta), val(ref_meta), [file(fastq)], file(reference), val(report_meta), fai, picard]
                    ^^

Warning: subworkflows/local/variant_analysis/main.nf:153:28: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [it[0], it[2], it[1]] + it[3..5] + [it[7]] } // [val(meta), val(ref_meta), [file(fastq)], file(reference), val(report_meta), fai, picard]
                           ^^

Warning: subworkflows/local/variant_analysis/main.nf:153:35: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [it[0], it[2], it[1]] + it[3..5] + [it[7]] } // [val(meta), val(ref_meta), [file(fastq)], file(reference), val(report_meta), fai, picard]
                                  ^^

Warning: subworkflows/local/variant_analysis/main.nf:153:44: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [it[0], it[2], it[1]] + it[3..5] + [it[7]] } // [val(meta), val(ref_meta), [file(fastq)], file(reference), val(report_meta), fai, picard]
                                           ^^

Warning: subworkflows/local/variant_analysis/main.nf:153:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .map { [it[0], it[2], it[1]] + it[3..5] + [it[7]] } // [val(meta), val(ref_meta), [file(fastq)], file(reference), val(report_meta), fai, picard]
                                                       ^^

Warning: subworkflows/local/variant_analysis/main.nf:156:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [it[0], it[7], it[8], it[1]] + it[3..6] }
                    ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:156:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [it[0], it[7], it[8], it[1]] + it[3..6] }
                           ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:156:35: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [it[0], it[7], it[8], it[1]] + it[3..6] }
                                  ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:156:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [it[0], it[7], it[8], it[1]] + it[3..6] }
                                         ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:156:51: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [it[0], it[7], it[8], it[1]] + it[3..6] }
                                                  ^^
```

Warning: subworkflows/local/variant_analysis/main.nf:161:87: Parameter was not used -- prefix with _ to suppress warning

        .collectFile(keepHeader: true, skip: 1) { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                      ^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:161:97: Parameter was not used -- prefix with _ to suppress warning

        .collectFile(keepHeader: true, skip: 1) { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                                ^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:161:104: Parameter was not used -- prefix with _ to suppress warning

        .collectFile(keepHeader: true, skip: 1) { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                                       ^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:161:116: Parameter was not used -- prefix with _ to suppress warning

        .collectFile(keepHeader: true, skip: 1) { sample_meta, report_meta, ref_meta, ref_path, usage, read_paths, sequence_type, ploidy ->
                                                                                                                   ^^^^^^^^^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:164:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it.getSimpleName(), it] }
                ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:164:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [it.getSimpleName(), it] }
                                    ^^
```

Warning: subworkflows/local/variant_analysis/main.nf:165:61: Parameter was not used -- prefix with _ to suppress warning

        .combine(CALL_VARIANTS.out.vcf.map { combined_meta, vcf -> [combined_meta.id, combined_meta]}, by: 0) // add on full combined metadata uing combined ID
                                                            ^^^

Warning: subworkflows/local/variant_analysis/main.nf:166:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { combined_id, ploidy_data_path, combined_meta ->
               ^^^^^^^^^^^
```
Warning: subworkflows/local/variant_analysis/main.nf:176:5: Variable was declared but not used
```
    removed_samps = VCF_TO_SNP_ALIGN.out.removed_sample_ids
    ^^^^^^^^^^^^^
```

Warning: subworkflows/local/variant_analysis/main.nf:178:22: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [[id: it[1].replace('\n', '')], it[0].group, it[0].ref, "VARIANT_ANALYSIS", "WARNING", "Sample removed from SNP phylogeny due to too much missing data."] } // meta, group_meta, ref_meta, workflow, level, message
                     ^^

Warning: subworkflows/local/variant_analysis/main.nf:178:48: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [[id: it[1].replace('\n', '')], it[0].group, it[0].ref, "VARIANT_ANALYSIS", "WARNING", "Sample removed from SNP phylogeny due to too much missing data."] } // meta, group_meta, ref_meta, workflow, level, message
                                               ^^

Warning: subworkflows/local/variant_analysis/main.nf:178:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map { [[id: it[1].replace('\n', '')], it[0].group, it[0].ref, "VARIANT_ANALYSIS", "WARNING", "Sample removed from SNP phylogeny due to too much missing data."] } // meta, group_meta, ref_meta, workflow, level, message
                                                            ^^

Warning: subworkflows/local/variant_analysis/main.nf:190:22: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, fasta -> [null, meta.group, meta.ref, "VARIANT_ANALYSIS", "WARNING", "Not enough samples to build a SNP tree."] }
                     ^^^^^

Warning: subworkflows/local/variant_analysis/main.nf:200:48: Implicit closure parameter is deprecated, declare an explicit parameter instead

    phylogeny = IQTREE_SNP.out.phylogeny.map{ [it[0].group, it[0].ref, it[1]] } // report_meta, ref_meta, tree
                                               ^^

Warning: subworkflows/local/variant_analysis/main.nf:200:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

    phylogeny = IQTREE_SNP.out.phylogeny.map{ [it[0].group, it[0].ref, it[1]] } // report_meta, ref_meta, tree
                                                            ^^

Warning: subworkflows/local/variant_analysis/main.nf:200:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

    phylogeny = IQTREE_SNP.out.phylogeny.map{ [it[0].group, it[0].ref, it[1]] } // report_meta, ref_meta, tree
                                                                       ^^

Warning: subworkflows/local/variant_analysis/main.nf:201:50: Implicit closure parameter is deprecated, declare an explicit parameter instead

    snp_align = VCF_TO_SNP_ALIGN.out.fasta.map{ [it[0].group, it[0].ref, it[1]] }
                                                 ^^

Warning: subworkflows/local/variant_analysis/main.nf:201:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

    snp_align = VCF_TO_SNP_ALIGN.out.fasta.map{ [it[0].group, it[0].ref, it[1]] }
                                                              ^^

Warning: subworkflows/local/variant_analysis/main.nf:201:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

    snp_align = VCF_TO_SNP_ALIGN.out.fasta.map{ [it[0].group, it[0].ref, it[1]] }
                                                                         ^^

Warning: subworkflows/local/variant_analysis/main.nf:202:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    vcf = CALL_VARIANTS.out.vcf.map{ [it[0].group, it[0].ref, it[1]] }
                                      ^^
```
Warning: subworkflows/local/variant_analysis/main.nf:202:52: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    vcf = CALL_VARIANTS.out.vcf.map{ [it[0].group, it[0].ref, it[1]] }
                                                   ^^
```

Warning: subworkflows/local/variant_analysis/main.nf:202:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

    vcf = CALL_VARIANTS.out.vcf.map{ [it[0].group, it[0].ref, it[1]] }
                                                              ^^

Warning: subworkflows/local/variant_analysis/main.nf:207:16: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [it[0].group, it[0].ref] + it[1..3] } // report_meta, ref_meta, vcf, align, tree
               ^^

Warning: subworkflows/local/variant_analysis/main.nf:207:29: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [it[0].group, it[0].ref] + it[1..3] } // report_meta, ref_meta, vcf, align, tree
                            ^^

Warning: subworkflows/local/variant_analysis/main.nf:207:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map{ [it[0].group, it[0].ref] + it[1..3] } // report_meta, ref_meta, vcf, align, tree
                                         ^^

Warning: workflows/pathogensurveillance.nf:150:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: workflows/pathogensurveillance.nf:150:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```

Warning: workflows/pathogensurveillance.nf:152:15: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, fastqc -> [report_meta, fastqc] }
              ^^^^^^^^^^^

Warning: workflows/pathogensurveillance.nf:156:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: workflows/pathogensurveillance.nf:156:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```

Warning: workflows/pathogensurveillance.nf:158:15: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, fastp_json -> [report_meta, fastp_json] }
              ^^^^^^^^^^^

Warning: workflows/pathogensurveillance.nf:162:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: workflows/pathogensurveillance.nf:162:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```

Warning: workflows/pathogensurveillance.nf:164:15: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, nanoplot_txt -> [report_meta, nanoplot_txt] }
              ^^^^^^^^^^^

Warning: workflows/pathogensurveillance.nf:168:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: workflows/pathogensurveillance.nf:168:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```

Warning: workflows/pathogensurveillance.nf:170:15: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, quast -> [report_meta, quast] }
              ^^^^^^^^^^^

Warning: workflows/pathogensurveillance.nf:174:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.report_group_ids]] }
                    ^^
```

Warning: workflows/pathogensurveillance.nf:198:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [[id: sample_meta.report_group_ids], sample_meta.findAll {it.key != 'paths' && it.key != 'ref_metas' && it.key != 'ref_ids'}]
                                                                      ^^

Warning: workflows/pathogensurveillance.nf:198:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [[id: sample_meta.report_group_ids], sample_meta.findAll {it.key != 'paths' && it.key != 'ref_metas' && it.key != 'ref_ids'}]
                                                                                           ^^

Warning: workflows/pathogensurveillance.nf:198:117: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [[id: sample_meta.report_group_ids], sample_meta.findAll {it.key != 'paths' && it.key != 'ref_metas' && it.key != 'ref_ids'}]
                                                                                                                    ^^

Warning: workflows/pathogensurveillance.nf:202:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [ "${report_meta.id}_sample_data.tsv", sample_meta.keySet().collect{'"' + it + '"'}.join('\t') + "\n" + sample_meta.values().collect{'"' + (it ?: '') + '"'}.join('\t') + "\n" ]
                                                                                      ^^

Warning: workflows/pathogensurveillance.nf:202:153: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [ "${report_meta.id}_sample_data.tsv", sample_meta.keySet().collect{'"' + it + '"'}.join('\t') + "\n" + sample_meta.values().collect{'"' + (it ?: '') + '"'}.join('\t') + "\n" ]
                                                                                                                                                        ^^

Warning: workflows/pathogensurveillance.nf:204:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName().replace('_sample_data', '')], it]}
                    ^^
```

Warning: workflows/pathogensurveillance.nf:204:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map {[[id: it.getSimpleName().replace('_sample_data', '')], it]}
                                                                     ^^

Warning: workflows/pathogensurveillance.nf:213:45: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [report_meta, ref_meta.findAll {it.key != 'ref_path' && it.key != 'gff'}]
                                            ^^

Warning: workflows/pathogensurveillance.nf:213:69: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [report_meta, ref_meta.findAll {it.key != 'ref_path' && it.key != 'gff'}]
                                                                    ^^

Warning: workflows/pathogensurveillance.nf:217:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [ "${report_meta.id}_reference_data.tsv", ref_meta.keySet().collect{'"' + it + '"'}.join('\t') + "\n" + ref_meta.values().collect{'"' + (it ?: '') + '"'}.join('\t') + "\n" ]
                                                                                      ^^

Warning: workflows/pathogensurveillance.nf:217:150: Implicit closure parameter is deprecated, declare an explicit parameter instead

            [ "${report_meta.id}_reference_data.tsv", ref_meta.keySet().collect{'"' + it + '"'}.join('\t') + "\n" + ref_meta.values().collect{'"' + (it ?: '') + '"'}.join('\t') + "\n" ]
                                                                                                                                                     ^^

Warning: workflows/pathogensurveillance.nf:219:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName().replace('_reference_data', '')], it]}
                    ^^
```

Warning: workflows/pathogensurveillance.nf:219:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .map {[[id: it.getSimpleName().replace('_reference_data', '')], it]}
                                                                        ^^

Warning: workflows/pathogensurveillance.nf:223:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: workflows/pathogensurveillance.nf:223:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```

Warning: workflows/pathogensurveillance.nf:225:15: Parameter was not used -- prefix with _ to suppress warning

        .map{ sample_meta, report_meta, sendsketch -> [report_meta, sendsketch] }
              ^^^^^^^^^^^

Warning: workflows/pathogensurveillance.nf:231:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: workflows/pathogensurveillance.nf:231:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```

Warning: workflows/pathogensurveillance.nf:234:16: Parameter was not used -- prefix with _ to suppress warning

        .map { sample_meta, report_meta, family_stats ->
               ^^^^^^^^^^^

Warning: workflows/pathogensurveillance.nf:240:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                    ^^
```
Warning: workflows/pathogensurveillance.nf:240:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ [[id: it.sample_id], [id: it.report_group_ids]] }
                                        ^^
```
Warning: workflows/pathogensurveillance.nf:242:15: Parameter was not used -- prefix with _ to suppress warning
```
        .map{ sample_meta, report_meta, ref_meta_file ->
              ^^^^^^^^^^^
```
Warning: workflows/pathogensurveillance.nf:247:50: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            [report_meta, ref_meta_files.findAll{it != null}]
                                                 ^^
```

Warning: workflows/pathogensurveillance.nf:252:29: Parameter was not used -- prefix with _ to suppress warning

        .map { report_meta, ref_meta, fasta -> [report_meta, fasta] }
                            ^^^^^^^^

Warning: workflows/pathogensurveillance.nf:257:29: Parameter was not used -- prefix with _ to suppress warning

        .map { report_meta, ref_meta, tree -> [report_meta, tree] }
                            ^^^^^^^^

Warning: workflows/pathogensurveillance.nf:266:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName()], it]}
                    ^^
```
Warning: workflows/pathogensurveillance.nf:266:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map {[[id: it.getSimpleName()], it]}
                                         ^^
```
Warning: workflows/pathogensurveillance.nf:286:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{it[0] != null}
                ^^
```
Warning: workflows/pathogensurveillance.nf:287:15: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ it.size() == 16 ? it + [null] : it }
              ^^
```
Warning: workflows/pathogensurveillance.nf:287:33: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ it.size() == 16 ? it + [null] : it }
                                ^^
```
Warning: workflows/pathogensurveillance.nf:287:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ it.size() == 16 ? it + [null] : it }
                                              ^^
```
Warning: workflows/pathogensurveillance.nf:288:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it.size() == 17 }
                 ^^
```
Warning: workflows/pathogensurveillance.nf:289:15: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ it.collect{ it ?: [] } }
              ^^
```
Warning: workflows/pathogensurveillance.nf:289:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ it.collect{ it ?: [] } }
                          ^^
```

Warning: workflows/pathogensurveillance.nf:337:34: Implicit closure parameter is deprecated, declare an explicit parameter instead

            sample_meta.findAll {it.key != 'paths' && it.key != 'ref_metas' && it.key != 'ref_ids'}
                                 ^^

Warning: workflows/pathogensurveillance.nf:337:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

            sample_meta.findAll {it.key != 'paths' && it.key != 'ref_metas' && it.key != 'ref_ids'}
                                                      ^^

Warning: workflows/pathogensurveillance.nf:337:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

            sample_meta.findAll {it.key != 'paths' && it.key != 'ref_metas' && it.key != 'ref_ids'}
                                                                               ^^

Warning: workflows/pathogensurveillance.nf:346:48: Implicit closure parameter is deprecated, declare an explicit parameter instead

            sample_meta.keySet().collect{'"' + it + '"'}.join('\t') + "\n" + sample_meta.values().collect{'"' + (it ?: '') + '"'}.join('\t') + "\n"
                                               ^^

Warning: workflows/pathogensurveillance.nf:346:114: Implicit closure parameter is deprecated, declare an explicit parameter instead

            sample_meta.keySet().collect{'"' + it + '"'}.join('\t') + "\n" + sample_meta.values().collect{'"' + (it ?: '') + '"'}.join('\t') + "\n"
                                                                                                                 ^^

Warning: workflows/pathogensurveillance.nf:356:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ref_meta[0].findAll {it.key != 'ref_path' && it.key != 'gff'}
                                 ^^
```

Warning: workflows/pathogensurveillance.nf:356:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ref_meta[0].findAll {it.key != 'ref_path' && it.key != 'gff'}
                                                         ^^

Warning: workflows/pathogensurveillance.nf:365:45: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ref_meta.keySet().collect{'"' + it + '"'}.join('\t') + "\n" + ref_meta.values().collect{'"' + (it ?: '') + '"'}.join('\t') + "\n"
                                            ^^

Warning: workflows/pathogensurveillance.nf:365:108: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ref_meta.keySet().collect{'"' + it + '"'}.join('\t') + "\n" + ref_meta.values().collect{'"' + (it ?: '') + '"'}.join('\t') + "\n"
                                                                                                           ^^

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nextflow lint results

❌ Errors

⚠️ Warnings

FilesExpand file tree

pathogensurveillance_lint.md

Latest commit

History

pathogensurveillance_lint.md

File metadata and controls

Nextflow lint results

❌ Errors

⚠️ Warnings