Nextflow lint results

Generated: 2026-01-16T10:24:29.834982671Z
Nextflow version: 25.12.0-edge
Summary: 31 errors, 158 warnings

❌ Errors

Error: conf/modules.config:179:21: Unexpected input: '{'

            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                    ^

Error: main.nf:20:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/multiplesequencealign/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf'

include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_multiplesequencealign_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:21:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/multiplesequencealign/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf'

include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_multiplesequencealign_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:64:5: PIPELINE_INITIALISATION is not defined

    PIPELINE_INITIALISATION (
    ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:78:9: PIPELINE_INITIALISATION is not defined

        PIPELINE_INITIALISATION.out.samplesheet,
        ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:79:9: PIPELINE_INITIALISATION is not defined

        PIPELINE_INITIALISATION.out.tools
        ^^^^^^^^^^^^^^^^^^^^^^^

Error: main.nf:85:5: PIPELINE_COMPLETION is not defined

    PIPELINE_COMPLETION (
    ^^^^^^^^^^^^^^^^^^^

Error: modules/nf-core/mafft/align/main.nf:29:9: add is already declared

    def add          = add             ? "--add <(unpigz -cdf ${add})"                   : ''
        ^^^

Error: modules/nf-core/mafft/align/main.nf:30:9: addfragments is already declared

    def addfragments = addfragments    ? "--addfragments <(unpigz -cdf ${addfragments})" : ''
        ^^^^^^^^^^^^

Error: modules/nf-core/mafft/align/main.nf:31:9: addfull is already declared

    def addfull      = addfull         ? "--addfull <(unpigz -cdf ${addfull})"           : ''
        ^^^^^^^

Error: modules/nf-core/mafft/align/main.nf:32:9: addprofile is already declared

    def addprofile   = addprofile      ? "--addprofile <(unpigz -cdf ${addprofile})"     : ''
        ^^^^^^^^^^

Error: modules/nf-core/mafft/align/main.nf:33:9: addlong is already declared

    def addlong      = addlong         ? "--addlong <(unpigz -cdf ${addlong})"           : ''
        ^^^^^^^

Error: modules/nf-core/mafft/align/main.nf:59:9: add is already declared

    def add          = add             ? "--add ${add}"                   : ''
        ^^^

Error: modules/nf-core/mafft/align/main.nf:60:9: addfragments is already declared

    def addfragments = addfragments    ? "--addfragments ${addfragments}" : ''
        ^^^^^^^^^^^^

Error: modules/nf-core/mafft/align/main.nf:61:9: addfull is already declared

    def addfull      = addfull         ? "--addfull ${addfull}"           : ''
        ^^^^^^^

Error: modules/nf-core/mafft/align/main.nf:62:9: addprofile is already declared

    def addprofile   = addprofile      ? "--addprofile ${addprofile}"     : ''
        ^^^^^^^^^^

Error: modules/nf-core/mafft/align/main.nf:63:9: addlong is already declared

    def addlong      = addlong         ? "--addlong ${addlong}"           : ''
        ^^^^^^^

Error: nextflow.config:341:1: Variable declarations cannot be mixed with config statements

def co2_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: nextflow.config:344:72: co2_timestamp is not defined

    traceFile   = "${params.outdir}/pipeline_info/co2footprint_trace_${co2_timestamp}.txt"
                                                                       ^^^^^^^^^^^^^

Error: nextflow.config:345:73: co2_timestamp is not defined

    reportFile  = "${params.outdir}/pipeline_info/co2footprint_report_${co2_timestamp}.html"
                                                                        ^^^^^^^^^^^^^

Error: nextflow.config:346:74: co2_timestamp is not defined

    summaryFile = "${params.outdir}/pipeline_info/co2footprint_summary_${co2_timestamp}.txt"
                                                                         ^^^^^^^^^^^^^

Error: nextflow.config:364:45: manifest is not defined

\033[0;35m  nf-core/multiplesequencealign ${manifest.version}\033[0m
                                            ^^^^^^^^

Error: nextflow.config:367:26: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                         ^^^^^^^^

Error: nextflow.config:367:69: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                    ^^^^^^^^

Error: nextflow.config:367:186: manifest is not defined

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                                                                         ^^^^^^^^

Error: nextflow.config:376:22: validation is not defined

        beforeText = validation.help.beforeText
                     ^^^^^^^^^^

Error: nextflow.config:377:21: validation is not defined

        afterText = validation.help.afterText
                    ^^^^^^^^^^

Error: subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf:570:66: Unexpected input: '='

    def traceTrees = prepTrace(cleanTraceData, suffix_to_replace = "_GUIDETREE", subworkflow = "COMPUTE_TREES", keys)
                                                                 ^

Error: workflows/multiplesequencealign.nf:10:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/multiplesequencealign/subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf'
```
include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_multiplesequencealign_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/multiplesequencealign.nf:311:13: Variables in a closure should be declared with def
```
            content =  meta.keySet().collect{it}.join(",")
            ^^^^^^^
```

Error: workflows/multiplesequencealign.nf:390:13: methodsDescriptionText is not defined

            methodsDescriptionText(ch_multiqc_custom_methods_description))
            ^^^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/custom/calculate_gaps/main.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/calculate_seqstats/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/create_template/main.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/extract_plddt/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/parse_irmsd/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/parse_sim/main.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/prepare_multiqc/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/prepare_shiny/main.nf:23:9: Variable was declared but not used
```
    def args         = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/custom/prepare_shiny/main.nf:24:5: Variable was declared but not used
```
    prefix           = task.ext.prefix ?: "${meta.id}"
    ^^^^^^
```
Warning: modules/nf-core/clustalo/align/main.nf:60:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/clustalo/guidetree/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/famsa/guidetree/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/foldmason/createdb/main.nf:37:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/foldmason/easymsa/main.nf:52:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/foldmason/msa2lddtreport/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/kalign/align/main.nf:59:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/learnmsa/align/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/mafft/align/main.nf:57:9: Variable was declared but not used

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

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

    def add          = add             ? "--add ${add}"                   : ''
        ^^^

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

    def addfragments = addfragments    ? "--addfragments ${addfragments}" : ''
        ^^^^^^^^^^^^

Warning: modules/nf-core/mafft/align/main.nf:61:9: Variable was declared but not used

    def addfull      = addfull         ? "--addfull ${addfull}"           : ''
        ^^^^^^^

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

    def addprofile   = addprofile      ? "--addprofile ${addprofile}"     : ''
        ^^^^^^^^^^

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

    def addlong      = addlong         ? "--addlong ${addlong}"           : ''
        ^^^^^^^

Warning: modules/nf-core/mafft/guidetree/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/magus/align/main.nf:47:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/mtmalign/align/main.nf:25:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/muscle5/super5/main.nf:52:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/pigz/compress/main.nf:35:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/pigz/uncompress/main.nf:39:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/tcoffee/alncompare/main.nf:58:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/tcoffee/extractfrompdb/main.nf:40:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/tcoffee/irmsd/main.nf:44:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/tcoffee/seqreformat/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/tcoffee/tcs/main.nf:23:9: Variable was declared but not used
```
    def args          = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/tcoffee/tcs/main.nf:63:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/upp/align/main.nf:23:9: Variable was declared but not used
```
    def tree_args = tree ? "-t $tree" : ""
        ^^^^^^^^^
```

Warning: nextflow.config:367:129: Implicit closure parameter is deprecated, declare an explicit parameter instead

        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
                                                                                                                                ^^

Warning: subworkflows/local/ALIGN/main.nf:40:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_msa      = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/ALIGN/main.nf:41:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/ALIGN/main.nf:81:13: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it[1] != null
            ^^
```
Warning: subworkflows/local/ALIGN/main.nf:92:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            clustalo:   it[0]["aligner"] == "CLUSTALO"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:93:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            famsa:      it[0]["aligner"] == "FAMSA"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:94:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            kalign:     it[0]["aligner"] == "KALIGN"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:95:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            learnmsa:   it[0]["aligner"] == "LEARNMSA"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:96:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            mafft:      it[0]["aligner"] == "MAFFT"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:97:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            magus:      it[0]["aligner"] == "MAGUS"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:98:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            muscle5:    it[0]["aligner"] == "MUSCLE5"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:99:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            mtmalign:   it[0]["aligner"] == "MTMALIGN"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:100:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            regressive: it[0]["aligner"] == "REGRESSIVE"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:101:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            tcoffee:    it[0]["aligner"] == "TCOFFEE"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:102:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            tcoffee3d:  it[0]["aligner"] == "3DCOFFEE"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:103:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            upp:        it[0]["aligner"] == "UPP"
                        ^^
```
Warning: subworkflows/local/ALIGN/main.nf:114:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            mtmalign: it[0]["aligner"] == "MTMALIGN"
                      ^^
```
Warning: subworkflows/local/ALIGN/main.nf:127:13: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it.size() == 5
            ^^
```
Warning: subworkflows/local/ALIGN/main.nf:134:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            foldmason: it[0]["aligner"] == "FOLDMASON"
                       ^^
```

Warning: subworkflows/local/ALIGN/main.nf:184:30: Parameter was not used -- prefix with _ to suppress warning

            meta, fastafile, treefile ->
                             ^^^^^^^^

Warning: subworkflows/local/ALIGN/main.nf:199:30: Parameter was not used -- prefix with _ to suppress warning

            meta, fastafile, treefile ->
                             ^^^^^^^^

Warning: subworkflows/local/ALIGN/main.nf:221:30: Parameter was not used -- prefix with _ to suppress warning

            meta, fastafile, treefile ->
                             ^^^^^^^^

Warning: subworkflows/local/ALIGN/main.nf:258:30: Parameter was not used -- prefix with _ to suppress warning

            meta, fastafile, treefile ->
                             ^^^^^^^^

Warning: subworkflows/local/ALIGN/main.nf:331:17: Parameter was not used -- prefix with _ to suppress warning

                merging_id, meta, fastafile, treefile, templatefile, datafiles ->
                ^^^^^^^^^^

Warning: subworkflows/local/ALIGN/main.nf:352:23: Parameter was not used -- prefix with _ to suppress warning

                meta, template, dependency ->
                      ^^^^^^^^

Warning: subworkflows/local/ALIGN/main.nf:369:29: Parameter was not used -- prefix with _ to suppress warning

                meta, tree, template, dependency ->
                            ^^^^^^^^

Warning: subworkflows/local/ALIGN/main.nf:388:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter { it[1].size() > 1 }
                      ^^
```

Warning: subworkflows/local/COMPUTE_TREES/main.nf:16:5: Parameter was not used -- prefix with _ to suppress warning

    ch_optional_data //channel: [ meta, template, [ /path/to/file1, /path/to/file2, ... ] ]
    ^^^^^^^^^^^^^^^^

Warning: subworkflows/local/COMPUTE_TREES/main.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/COMPUTE_TREES/main.nf:21:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_trees    = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/COMPUTE_TREES/main.nf:33:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            famsa:    it[0]["tree"] == "FAMSA"
                      ^^
```
Warning: subworkflows/local/COMPUTE_TREES/main.nf:34:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            clustalo: it[0]["tree"] == "CLUSTALO"
                      ^^
```
Warning: subworkflows/local/COMPUTE_TREES/main.nf:35:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            mafft:    it[0]["tree"] == "MAFFT"
                      ^^
```
Warning: subworkflows/local/EVALUATE/main.nf:28:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions     = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:29:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    sp_csv          = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:30:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tc_csv          = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:31:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    irmsd_csv       = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:32:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    tcs_csv         = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:33:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    gaps_csv        = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:34:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_eval_summary = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:66:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, csv -> csv
                ^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:87:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, csv ->
                ^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:114:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, csv ->
                ^^^^
```

Warning: subworkflows/local/EVALUATE/main.nf:163:53: Parameter was not used -- prefix with _ to suppress warning

                                                    meta, csv -> csv
                                                    ^^^^

Warning: subworkflows/local/EVALUATE/main.nf:169:9: Variable was declared but not used

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

Warning: subworkflows/local/EVALUATE/main.nf:186:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, csv ->
                ^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:206:31: Parameter was not used -- prefix with _ to suppress warning
```
    sp      = sp_csv.map    { meta, csv -> csv }
                              ^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:207:31: Parameter was not used -- prefix with _ to suppress warning
```
    tc      = tc_csv.map    { meta, csv -> csv }
                              ^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:208:31: Parameter was not used -- prefix with _ to suppress warning
```
    irmsd   = irmsd_csv.map { meta, csv -> csv }
                              ^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:209:31: Parameter was not used -- prefix with _ to suppress warning
```
    gaps    = gaps_csv.map  { meta, csv -> csv }
                              ^^^^
```
Warning: subworkflows/local/EVALUATE/main.nf:210:31: Parameter was not used -- prefix with _ to suppress warning
```
    tcs     = tcs_csv.map   { meta, csv -> csv }
                              ^^^^
```
Warning: subworkflows/local/PREPROCESS/main.nf:10:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/PREPROCESS/main.nf:11:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_preprocessed_data = Channel.empty()
                           ^^^^^^^
```
Warning: subworkflows/local/STATS/main.nf:20:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions      = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/STATS/main.nf:21:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    sim_csv          = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/STATS/main.nf:22:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    seqstats_csv     = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/STATS/main.nf:23:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    plddts_csv       = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/STATS/main.nf:24:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_stats_summary = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/STATS/main.nf:39:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, csv ->
                ^^^^
```
Warning: subworkflows/local/STATS/main.nf:70:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, csv ->
                ^^^^
```
Warning: subworkflows/local/STATS/main.nf:99:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, csv -> csv
                ^^^^
```
Warning: subworkflows/local/STATS/main.nf:121:35: Parameter was not used -- prefix with _ to suppress warning
```
    sim      = sim_csv.map      { meta, csv -> csv }
                                  ^^^^
```
Warning: subworkflows/local/STATS/main.nf:122:35: Parameter was not used -- prefix with _ to suppress warning
```
    seqstats = seqstats_csv.map { meta, csv -> csv }
                                  ^^^^
```
Warning: subworkflows/local/STATS/main.nf:123:35: Parameter was not used -- prefix with _ to suppress warning
```
    plddts   = plddts_csv.map   { meta, csv -> csv }
                                  ^^^^
```
Warning: subworkflows/local/STATS/main.nf:139:14: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ].count{ it == true }
             ^^
```
Warning: subworkflows/local/TEMPLATES/main.nf:12:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/TEMPLATES/main.nf:17:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            template: it[2] != null
                      ^^
```

Warning: subworkflows/local/TEMPLATES/main.nf:26:36: Parameter was not used -- prefix with _ to suppress warning

                meta,optional_data,template ->
                                   ^^^^^^^^

Warning: subworkflows/local/TEMPLATES/main.nf:35:18: Parameter was not used -- prefix with _ to suppress warning
```
            meta,optional_data,template ->
                 ^^^^^^^^^^^^^
```
Warning: subworkflows/local/VISUALIZATION/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/VISUALIZATION/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_html     = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/VISUALIZATION/main.nf:25:13: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it.size() == 4
            ^^
```

Warning: subworkflows/local/VISUALIZATION/main.nf:28:13: Parameter was not used -- prefix with _ to suppress warning

            tree_meta, meta, msa, tree -> [ meta.subMap(["id"]), meta, msa, tree ]
            ^^^^^^^^^

Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:98: The use of Channel to access channel factories is deprecated -- use channel instead

    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
                                                                                                 ^^^^^^^

Warning: workflows/multiplesequencealign.nf:63:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files             = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:64:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_report            = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:65:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    evaluation_summary           = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:66:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    stats_summary                = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:67:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    stats_and_evaluation_summary = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:68:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_refs                      = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:69:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_templates                 = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:70:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_optional_data             = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:71:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions                  = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:74:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[1].size() > 0}
                  ^^
```

Warning: workflows/multiplesequencealign.nf:76:26: Parameter was not used -- prefix with _ to suppress warning

            meta, fasta, ref, str, template ->
                         ^^^

Warning: workflows/multiplesequencealign.nf:76:31: Parameter was not used -- prefix with _ to suppress warning

            meta, fasta, ref, str, template ->
                              ^^^

Warning: workflows/multiplesequencealign.nf:76:36: Parameter was not used -- prefix with _ to suppress warning

            meta, fasta, ref, str, template ->
                                   ^^^^^^^^

Warning: workflows/multiplesequencealign.nf:82:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[2].size() > 0}
                  ^^
```
Warning: workflows/multiplesequencealign.nf:84:19: Parameter was not used -- prefix with _ to suppress warning
```
            meta, fasta, ref, str, template ->
                  ^^^^^
```

Warning: workflows/multiplesequencealign.nf:84:31: Parameter was not used -- prefix with _ to suppress warning

            meta, fasta, ref, str, template ->
                              ^^^

Warning: workflows/multiplesequencealign.nf:84:36: Parameter was not used -- prefix with _ to suppress warning

            meta, fasta, ref, str, template ->
                                   ^^^^^^^^

Warning: workflows/multiplesequencealign.nf:90:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[4].size() > 0}
                  ^^
```
Warning: workflows/multiplesequencealign.nf:92:19: Parameter was not used -- prefix with _ to suppress warning
```
            meta, fasta, ref, str, template ->
                  ^^^^^
```

Warning: workflows/multiplesequencealign.nf:92:26: Parameter was not used -- prefix with _ to suppress warning

            meta, fasta, ref, str, template ->
                         ^^^

Warning: workflows/multiplesequencealign.nf:92:31: Parameter was not used -- prefix with _ to suppress warning

            meta, fasta, ref, str, template ->
                              ^^^

Warning: workflows/multiplesequencealign.nf:119:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
            pdbs_dir = Channel.fromPath(params.pdbs_dir)
                       ^^^^^^^
```

Warning: workflows/multiplesequencealign.nf:124:24: Parameter was not used -- prefix with _ to suppress warning

                .map { meta, dir -> [ file(dir).listFiles() ] }
                       ^^^^

Warning: workflows/multiplesequencealign.nf:132:42: The use of Channel to access channel factories is deprecated -- use channel instead

            optional_data_to_be_mapped = Channel.fromPath(params.pdbs_dir+"/**")
                                         ^^^^^^^

Warning: workflows/multiplesequencealign.nf:158:24: Parameter was not used -- prefix with _ to suppress warning

                .map { dep_id, dep, fasta_id -> [ fasta_id, dep ] }
                       ^^^^^^

Warning: workflows/multiplesequencealign.nf:168:23: Parameter was not used -- prefix with _ to suppress warning

                meta, fasta, ref, str, template ->
                      ^^^^^

Warning: workflows/multiplesequencealign.nf:168:30: Parameter was not used -- prefix with _ to suppress warning

                meta, fasta, ref, str, template ->
                             ^^^

Warning: workflows/multiplesequencealign.nf:168:40: Parameter was not used -- prefix with _ to suppress warning

                meta, fasta, ref, str, template ->
                                       ^^^^^^^^

Warning: workflows/multiplesequencealign.nf:171:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .filter { it[1].size() > 0 }
                      ^^
```
Warning: workflows/multiplesequencealign.nf:178:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                compressed:   it[1].endsWith('.tar.gz')
                              ^^
```
Warning: workflows/multiplesequencealign.nf:202:13: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it[-1] == null
            ^^
```
Warning: workflows/multiplesequencealign.nf:242:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[3]["aligner"] == "3DCOFFEE" }
                  ^^
```
Warning: workflows/multiplesequencealign.nf:249:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_optional_data_template = Channel.empty()
                                ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:263:13: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            it[-1] == null
            ^^
```

Warning: workflows/multiplesequencealign.nf:310:80: Parameter was not used -- prefix with _ to suppress warning

        ALIGN.out.msa.collectFile(keepHeader: true, skip: 1,sort: true){ meta, msa ->
                                                                               ^^^

Warning: workflows/multiplesequencealign.nf:311:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            content =  meta.keySet().collect{it}.join(",")
                                             ^^
```
Warning: workflows/multiplesequencealign.nf:313:46: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            content += meta.values().collect{it}.join(",")
                                             ^^
```

Warning: workflows/multiplesequencealign.nf:328:48: Parameter was not used -- prefix with _ to suppress warning

        stats_summary_csv = stats_summary.map{ meta, csv -> csv }
                                               ^^^^

Warning: workflows/multiplesequencealign.nf:329:53: Parameter was not used -- prefix with _ to suppress warning

        eval_summary_csv  = evaluation_summary.map{ meta, csv -> csv }
                                                    ^^^^

Warning: workflows/multiplesequencealign.nf:346:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
        shiny_app = Channel.fromPath(params.shiny_app)
                    ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:372:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_multiqc_config        = Channel.fromPath(
                                   ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:375:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.multiqc_config, checkIfExists: true) :
            ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:376:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:378:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
            ^^^^^^^
```
Warning: workflows/multiplesequencealign.nf:379:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```

Warning: workflows/multiplesequencealign.nf:383:49: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/multiplesequencealign.nf:389:49: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_methods_description                = Channel.value(
                                                ^^^^^^^

Warning: workflows/multiplesequencealign.nf:401:112: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files                      = ch_multiqc_files.mix(PREPARE_MULTIQC.out.multiqc_table.collect{it[1]}.ifEmpty([]))
                                                                                                               ^^

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