Nextflow lint results

Generated: 2026-02-16T00:19:47.188987641Z
Nextflow version: 26.01.1-edge
Summary: 12 errors, 46 warnings

❌ Errors

Error: modules/nf-core/quartonotebook/parametrize.nf:1:1: Groovy import declarations are not supported -- use fully-qualified name inline instead
```
import org.yaml.snakeyaml.Yaml
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: modules/nf-core/quartonotebook/parametrize.nf:2:1: Groovy import declarations are not supported -- use fully-qualified name inline instead
```
import org.yaml.snakeyaml.DumperOptions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: modules/nf-core/quartonotebook/parametrize.nf:21:29: DumperOptions is not defined

    DumperOptions options = new DumperOptions();
                            ^^^^^^^^^^^^^^^^^^^

Error: modules/nf-core/quartonotebook/parametrize.nf:22:33: DumperOptions is not defined

    options.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK);
                                ^^^^^^^^^^^^^

Error: modules/nf-core/quartonotebook/parametrize.nf:23:16: Yaml is not defined
```
    def yaml = new Yaml(options)
               ^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/kraken2_classification/main.nf:25:20: kraken2_db is already declared

            .map { kraken2_db ->
                   ^^^^^^^^^^

Error: subworkflows/local/prepare_genome_indices/main.nf:48:49: igenome is not defined

        genome_meta = [meta, file(params.genomes[ igenome ][ fasta ]), path(params.genomes[ igenome ][ bowtie2 ])]
                                                ^^^^^^^^^^^

Error: subworkflows/local/prepare_genome_indices/main.nf:48:60: fasta is not defined

        genome_meta = [meta, file(params.genomes[ igenome ][ fasta ]), path(params.genomes[ igenome ][ bowtie2 ])]
                                                           ^^^^^^^^^

Error: subworkflows/local/prepare_genome_indices/main.nf:48:72: path is not defined

        genome_meta = [meta, file(params.genomes[ igenome ][ fasta ]), path(params.genomes[ igenome ][ bowtie2 ])]
                                                                       ^^^^

Error: subworkflows/local/prepare_genome_indices/main.nf:48:91: igenome is not defined

        genome_meta = [meta, file(params.genomes[ igenome ][ fasta ]), path(params.genomes[ igenome ][ bowtie2 ])]
                                                                                          ^^^^^^^^^^^

Error: subworkflows/local/prepare_genome_indices/main.nf:48:102: bowtie2 is not defined

        genome_meta = [meta, file(params.genomes[ igenome ][ fasta ]), path(params.genomes[ igenome ][ bowtie2 ])]
                                                                                                     ^^^^^^^^^^^

Error: subworkflows/local/quarto_reporting/main.nf:26:9: coproid_notebook is already declared
```
        coproid_notebook ->
        ^^^^^^^^^^^^^^^^
```

⚠️ Warnings

Warning: modules/local/create_acc2tax/main.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ""
        ^^^^
```
Warning: modules/local/damageprofiler/merge/main.nf:17:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```
Warning: modules/local/kraken/merge/main.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```
Warning: modules/local/kraken/parse/main.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```
Warning: modules/local/pydamage/merge/main.nf:17:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```
Warning: modules/local/sam2lca/merge/main.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args   ?: ''
        ^^^^
```
Warning: modules/local/sam2lca/prep_db/main.nf:19:9: Variable was declared but not used
```
    def args = task.ext.args ?: ""
        ^^^^
```
Warning: modules/nf-core/kraken2/kraken2/main.nf:60:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

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

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

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

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

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

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

Warning: modules/nf-core/quartonotebook/main.nf:102:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/sourcepredict/main.nf:47:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/align_index/main.nf:9:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/kraken2_classification/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/kraken2_classification/main.nf:23:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel
        ^^^^^^^
```
Warning: subworkflows/local/kraken2_classification/main.nf:82:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        sqlite = XZ_DECOMPRESS.out.file.map { it[1] }
                                              ^^
```
Warning: subworkflows/local/merge_sort_index_samtools/main.nf:10:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome_indices/main.nf:9:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome_indices/main.nf:12:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_genome_channel(it) }
                                     ^^
```
Warning: subworkflows/local/prepare_genome_indices/main.nf:17:26: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            index_avail: it.size() > 2
                         ^^
```
Warning: subworkflows/local/prepare_genome_indices/main.nf:18:29: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            no_index_avail: it.size() == 2
                            ^^
```
Warning: subworkflows/local/quarto_reporting/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/quarto_reporting/main.nf:20:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    extensions = Channel.fromPath("${projectDir}/assets/_extensions").collect()
                 ^^^^^^^
```
Warning: subworkflows/local/quarto_reporting/main.nf:23:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/local/sam2lca_db/main.nf:15:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_coproid_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_coproid_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_coproid_pipeline/main.nf:39:5: Parameter was not used -- prefix with _ to suppress warning
```
    genome_sheet //  string: Path to reference genomesheet
    ^^^^^^^^^^^^
```

Warning: workflows/coproid.nf:71:70: 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/coproid.nf:83:5: Variable was declared but not used
```
    ch_trimmed = FASTP.out.reads
    ^^^^^^^^^^
```

Warning: workflows/coproid.nf:84:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.json.collect { it[1] })
                                                                     ^^

Warning: workflows/coproid.nf:115:85: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/coproid.nf:124:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(DAMAGEPROFILER.out.results.collect { it[1] })
                                                                                 ^^

Warning: workflows/coproid.nf:127:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .collect { it[1] }
                   ^^
```
Warning: workflows/coproid.nf:150:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .collect { it[1] }
                   ^^
```

Warning: workflows/coproid.nf:163:27: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, bam, bai ->
                          ^^^

Warning: workflows/coproid.nf:178:60: Parameter was not used -- prefix with _ to suppress warning

            PREPARE_GENOMES.out.genomes.map { meta, fasta, index ->
                                                           ^^^^^

Warning: workflows/coproid.nf:190:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_sam2lca_db = Channel.fromPath(params.sam2lca_db).first()
                        ^^^^^^^
```
Warning: workflows/coproid.nf:202:5: Variable was declared but not used
```
    ch_sam2lca = SAM2LCA_ANALYZE.out.csv
    ^^^^^^^^^^
```
Warning: workflows/coproid.nf:206:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .collect { it[1] }
                   ^^
```

Warning: workflows/coproid.nf:221:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_CLASSIFICATION.out.kraken_report.collect { it[1] })
                                                                                               ^^

Warning: workflows/coproid.nf:227:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def topic_versions = Channel
                         ^^^^^^^
```

Warning: workflows/coproid.nf:258:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

            KRAKEN2_CLASSIFICATION.out.sp_report.collectFile { it[1] },
                                                               ^^

Warning: workflows/coproid.nf:259:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

            KRAKEN2_CLASSIFICATION.out.sp_embedding.collectFile { it[1] },
                                                                  ^^

Warning: workflows/coproid.nf:262:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.genome_sheet),
            ^^^^^^^
```

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