Nextflow lint results

Generated: 2026-01-16T10:19:42.887568632Z
Nextflow version: 25.12.0-edge
Summary: 13 errors, 61 warnings

❌ Errors

Error: subworkflows/local/generate_downstream_samplesheets/main.nf:47:17: Variables in a closure should be declared with def
```
                new_meta = [
                ^^^^^^^^
```

Error: subworkflows/local/generate_downstream_samplesheets/main.nf:54:17: Variables in a closure should be declared with def

                read_files = reads.flatten().sort(false){ a, b -> a.getName().tokenize('.')[0] <=> b.getName().tokenize('.')[0] }
                ^^^^^^^^^^

Error: subworkflows/local/generate_downstream_samplesheets/main.nf:108:5: format_sep was assigned but not declared
```
    format_sep = ["csv":",", "tsv":"\t", "txt":"\t"][format]
    ^^^^^^^^^^
```
Error: subworkflows/local/generate_downstream_samplesheets/main.nf:110:5: ch_header was assigned but not declared
```
    ch_header = ch_list_for_samplesheet
    ^^^^^^^^^
```
Error: subworkflows/local/generate_downstream_samplesheets/main.nf:112:5: ch_header is not defined
```
    ch_header
    ^^^^^^^^^
```
Error: subworkflows/local/generate_downstream_samplesheets/main.nf:114:32: format_sep is not defined
```
        .map{ it.keySet().join(format_sep) }
                               ^^^^^^^^^^
```

Error: subworkflows/local/generate_downstream_samplesheets/main.nf:115:64: format_sep is not defined

        .concat( ch_list_for_samplesheet.map{ it.values().join(format_sep) })
                                                               ^^^^^^^^^^

Error: workflows/detaxizer.nf:46:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def ch_fasta_blastn = Channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/detaxizer.nf:48:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if ( !params.fasta_blastn && params.validation_blastn ) {
^
```
Error: workflows/detaxizer.nf:57:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def ch_fasta_bbduk = Channel.empty()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/detaxizer.nf:59:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if ( !params.fasta_bbduk && params.classification_bbduk ) {
^
```

Error: workflows/detaxizer.nf:212:13: ch_fasta_bbduk is not defined

            ch_fasta_bbduk.first()
            ^^^^^^^^^^^^^^

Error: workflows/detaxizer.nf:305:30: ch_fasta_blastn is not defined

        ch_reference_fasta = ch_fasta_blastn
                             ^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/nf-core/bbmap/bbduk/main.nf:48:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/blast/blastn/main.nf:65:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/blast/makeblastdb/main.nf:42:9: Variable was declared but not used
```
    def args           = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/kraken2/kraken2/main.nf:60:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

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

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

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

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

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

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

Warning: subworkflows/local/generate_downstream_samplesheets/main.nf:73:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it.short_reads_1!="" } // MAG doesn't support standalone long reads
                 ^^
```
Warning: subworkflows/local/generate_downstream_samplesheets/main.nf:75:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            se: it.short_reads_2 ==""
                ^^
```
Warning: subworkflows/local/generate_downstream_samplesheets/main.nf:81:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it.long_reads !="" && it.short_reads_1=="" }
                 ^^
```
Warning: subworkflows/local/generate_downstream_samplesheets/main.nf:81:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{ it.long_reads !="" && it.short_reads_1=="" }
                                       ^^
```

Warning: subworkflows/local/generate_downstream_samplesheets/main.nf:82:169: Implicit closure parameter is deprecated, declare an explicit parameter instead

        .collect{ log.warn("Standalone long reads are not yet supported by the nf-core/mag pipeline and ARE REMOVED from the samplesheet 'mag-{se,pe}.csv' \n sample: ${it.sample}" )}
                                                                                                                                                                        ^^

Warning: subworkflows/local/generate_downstream_samplesheets/main.nf:114:15: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map{ it.keySet().join(format_sep) }
              ^^
```
Warning: subworkflows/local/generate_downstream_samplesheets/main.nf:115:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .concat( ch_list_for_samplesheet.map{ it.values().join(format_sep) })
                                              ^^
```
Warning: subworkflows/local/utils_nfcore_detaxizer_pipeline/main.nf:32:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_detaxizer_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_detaxizer_pipeline/main.nf:42:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/utils_nfcore_detaxizer_pipeline/main.nf:67:144: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/utils_nfcore_detaxizer_pipeline/main.nf:104:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```

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/detaxizer.nf:46:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
def ch_fasta_blastn = Channel.empty()
                      ^^^^^^^
```
Warning: workflows/detaxizer.nf:49:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta_blastn = Channel.fromPath(getGenomeAttribute('fasta'))
                      ^^^^^^^
```
Warning: workflows/detaxizer.nf:52:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta_blastn = Channel.fromPath(params.fasta_blastn)
                      ^^^^^^^
```
Warning: workflows/detaxizer.nf:57:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
def ch_fasta_bbduk = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/detaxizer.nf:60:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta_bbduk = Channel.fromPath(getGenomeAttribute('fasta'))
                     ^^^^^^^
```
Warning: workflows/detaxizer.nf:63:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta_bbduk = Channel.fromPath(params.fasta_bbduk)
                     ^^^^^^^
```
Warning: workflows/detaxizer.nf:71:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/detaxizer.nf:72:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/detaxizer.nf:73:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_filtered_reads = Channel.empty()
                        ^^^^^^^
```
Warning: workflows/detaxizer.nf:74:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_removed_reads  = Channel.empty()
                        ^^^^^^^
```
Warning: workflows/detaxizer.nf:77:21: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        shortReads: it[1]
                    ^^
```

Warning: workflows/detaxizer.nf:79:57: Parameter was not used -- prefix with _ to suppress warning

        meta, short_reads_fastq_1, short_reads_fastq_2, long_reads_fastq_1 ->
                                                        ^^^^^^^^^^^^^^^^^^

Warning: workflows/detaxizer.nf:88:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        longReads: it[3]
                   ^^
```

Warning: workflows/detaxizer.nf:90:15: Parameter was not used -- prefix with _ to suppress warning

        meta, short_reads_fastq_1, short_reads_fastq_2, long_reads_fastq_1 ->
              ^^^^^^^^^^^^^^^^^^^

Warning: workflows/detaxizer.nf:90:36: Parameter was not used -- prefix with _ to suppress warning

        meta, short_reads_fastq_1, short_reads_fastq_2, long_reads_fastq_1 ->
                                   ^^^^^^^^^^^^^^^^^^^

Warning: workflows/detaxizer.nf:112:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/detaxizer.nf:140:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_kraken2_db = Channel.fromPath(params.kraken2db).map {
                        ^^^^^^^
```

Warning: workflows/detaxizer.nf:184:75: Parameter was not used -- prefix with _ to suppress warning

        ch_parsed_kraken2_report = PARSE_KRAKEN2REPORT.out.to_filter.map {meta, path -> path}
                                                                          ^^^^

Warning: workflows/detaxizer.nf:277:13: Parameter was not used -- prefix with _ to suppress warning
```
            meta, path -> [path]
            ^^^^
```
Warning: workflows/detaxizer.nf:398:17: Parameter was not used -- prefix with _ to suppress warning
```
                meta, path -> [path]
                ^^^^
```

Warning: workflows/detaxizer.nf:438:49: Parameter was not used -- prefix with _ to suppress warning

                ch_to_filter.map { meta, reads, ids -> tuple(meta, reads) },
                                                ^^^

Warning: workflows/detaxizer.nf:439:36: Parameter was not used -- prefix with _ to suppress warning

                ch_to_filter.map { meta, reads, ids -> ids.toString() },
                                   ^^^^

Warning: workflows/detaxizer.nf:439:42: Parameter was not used -- prefix with _ to suppress warning

                ch_to_filter.map { meta, reads, ids -> ids.toString() },
                                         ^^^^^

Warning: workflows/detaxizer.nf:440:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
                Channel.value('fastq.gz'),
                ^^^^^^^
```
Warning: workflows/detaxizer.nf:441:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
                Channel.value(false)
                ^^^^^^^
```

Warning: workflows/detaxizer.nf:447:53: Parameter was not used -- prefix with _ to suppress warning

                    ch_to_filter.map { meta, reads, ids -> tuple(meta, reads) },
                                                    ^^^

Warning: workflows/detaxizer.nf:448:40: Parameter was not used -- prefix with _ to suppress warning

                    ch_to_filter.map { meta, reads, ids -> ids.toString() },
                                       ^^^^

Warning: workflows/detaxizer.nf:448:46: Parameter was not used -- prefix with _ to suppress warning

                    ch_to_filter.map { meta, reads, ids -> ids.toString() },
                                             ^^^^^

Warning: workflows/detaxizer.nf:449:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
                    Channel.value('fastq.gz'),
                    ^^^^^^^
```
Warning: workflows/detaxizer.nf:450:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
                    Channel.value(false)
                    ^^^^^^^
```
Warning: workflows/detaxizer.nf:455:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_filter_removed = Channel.empty()
                                    ^^^^^^^
```
Warning: workflows/detaxizer.nf:473:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_removed2rename = Channel.empty()
                                ^^^^^^^
```

Warning: workflows/detaxizer.nf:496:110: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_removed_reads  = params.output_removed_reads ? RENAME_FASTQ_HEADERS_AFTER.out.fastq_removed : Channel.empty()
                                                                                                             ^^^^^^^

Warning: workflows/detaxizer.nf:501:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_removed_reads = Channel.empty()
                               ^^^^^^^
```
Warning: workflows/detaxizer.nf:580:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/detaxizer.nf:583:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/detaxizer.nf:584:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/detaxizer.nf:586:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/detaxizer.nf:587:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/detaxizer.nf:591:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

Warning: workflows/detaxizer.nf:597:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nextflow lint results

❌ Errors

⚠️ Warnings

FilesExpand file tree

detaxizer_lint.md

Latest commit

History

detaxizer_lint.md

File metadata and controls

Nextflow lint results

❌ Errors

⚠️ Warnings