Nextflow lint results

Generated: 2026-01-16T10:18:32.329072758Z
Nextflow version: 25.12.0-edge
Summary: 38 errors, 58 warnings

❌ Errors

Error: main.nf:19:1: Included name 'PIPELINE_INITIALISATION' is not defined in module '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/coproid/subworkflows/local/utils_nfcore_coproid_pipeline/main.nf'
```
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_coproid_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: main.nf:75:5: PIPELINE_INITIALISATION is not defined

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

Error: main.nf:89:9: PIPELINE_INITIALISATION is not defined

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

Error: main.nf:90:9: PIPELINE_INITIALISATION is not defined

        PIPELINE_INITIALISATION.out.genomesheet
        ^^^^^^^^^^^^^^^^^^^^^^^

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: modules/nf-core/sam2lca/analyze/main.nf:28:9: database is already declared

    def database = database ? "${database}" : "sam2lca_db"
        ^^^^^^^^

Error: modules/nf-core/sourcepredict/main.nf:29:9: save_embedding is already declared

    def save_embedding = save_embedding ? "-e ${prefix}.embedding.sourcepredict.csv" : ""
        ^^^^^^^^^^^^^^

Error: nextflow.config:215:1: Variable declarations cannot be mixed with config statements

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

Error: nextflow.config:218:68: trace_timestamp is not defined

    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
                                                                   ^^^^^^^^^^^^^^^

Error: nextflow.config:222:66: trace_timestamp is not defined

    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
                                                                 ^^^^^^^^^^^^^^^

Error: nextflow.config:226:65: trace_timestamp is not defined

    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
                                                                ^^^^^^^^^^^^^^^

Error: nextflow.config:230:62: trace_timestamp is not defined

    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
                                                             ^^^^^^^^^^^^^^^

Error: nextflow.config:290:31: manifest is not defined

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

Error: nextflow.config:293:26: 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:293:69: 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:293:186: 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:302:22: validation is not defined

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

Error: nextflow.config:303:21: validation is not defined

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

Error: subworkflows/local/kraken2_classification/main.nf:8:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_sp_sources      = file(params.sp_sources)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/kraken2_classification/main.nf:9:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_sp_labels       = file(params.sp_labels)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/kraken2_classification/main.nf:10:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_sqlite_traverse = file(params.taxa_sqlite_traverse_pkl)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/kraken2_classification/main.nf:24:17: kraken2_db is already declared
```
                kraken2_db -> [
                ^^^^^^^^^^
```
Error: subworkflows/local/kraken2_classification/main.nf:89:9: ch_sp_sources is not defined
```
        ch_sp_sources,
        ^^^^^^^^^^^^^
```
Error: subworkflows/local/kraken2_classification/main.nf:90:9: ch_sp_labels is not defined
```
        ch_sp_labels,
        ^^^^^^^^^^^^
```
Error: subworkflows/local/kraken2_classification/main.nf:92:9: ch_sqlite_traverse is not defined
```
        ch_sqlite_traverse,
        ^^^^^^^^^^^^^^^^^^
```

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 ->
        ^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_coproid_pipeline/main.nf:27:1: Invalid workflow definition -- check for missing or out-of-order section labels
```
workflow PIPELINE_INITIALISATION {
^
```
Error: workflows/coproid.nf:37:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_kraken2_db = file(params.kraken2_db)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/coproid.nf:212:9: ch_kraken2_db is not defined
```
        ch_kraken2_db
        ^^^^^^^^^^^^^
```

⚠️ 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/sam2lca/analyze/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/sourcepredict/main.nf:50:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: nextflow.config:293:129: 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_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:8:1: Variable was declared but not used
```
ch_sp_sources      = file(params.sp_sources)
^^^^^^^^^^^^^
```
Warning: subworkflows/local/kraken2_classification/main.nf:9:1: Variable was declared but not used
```
ch_sp_labels       = file(params.sp_labels)
^^^^^^^^^^^^
```
Warning: subworkflows/local/kraken2_classification/main.nf:10:1: Variable was declared but not used
```
ch_sqlite_traverse = file(params.taxa_sqlite_traverse_pkl)
^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/kraken2_classification/main.nf:18:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/kraken2_classification/main.nf:21:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel
            ^^^^^^^
```
Warning: subworkflows/local/kraken2_classification/main.nf:77:55: 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/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/coproid.nf:37:1: Variable was declared but not used
```
ch_kraken2_db = file(params.kraken2_db)
^^^^^^^^^^^^^
```
Warning: workflows/coproid.nf:53:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions      = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/coproid.nf:54:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/coproid.nf:71:68: 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/coproid.nf:84:5: Variable was declared but not used
```
    ch_trimmed       = FASTP.out.reads
    ^^^^^^^^^^
```

Warning: workflows/coproid.nf:85:68: 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:117:83: 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:126:80: 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:128:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    DAMAGEPROFILER.out.results.collect({it[1]})
                                        ^^
```
Warning: workflows/coproid.nf:148:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    PYDAMAGE_ANALYZE.out.csv.collect({it[1]})
                                      ^^
```

Warning: workflows/coproid.nf:160:20: Parameter was not used -- prefix with _ to suppress warning

        meta, bam, bai -> [['id':meta.sample_name], bam] // meta.id, bam
                   ^^^

Warning: workflows/coproid.nf:174:30: Parameter was not used -- prefix with _ to suppress warning

                meta, fasta, index -> [meta, fasta]
                             ^^^^^

Warning: workflows/coproid.nf:184:25: 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:196:5: Variable was declared but not used
```
    ch_sam2lca  = SAM2LCA_ANALYZE.out.csv
    ^^^^^^^^^^
```
Warning: workflows/coproid.nf:199:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    SAM2LCA_ANALYZE.out.csv.collect({it[1]})
                                     ^^
```

Warning: workflows/coproid.nf:214:94: 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:230:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/coproid.nf:231:65: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/coproid.nf:234:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.genome_sheet),
            ^^^^^^^
```
Warning: workflows/coproid.nf:249:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/coproid.nf:252:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/coproid.nf:253:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/coproid.nf:255:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/coproid.nf:256:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```

Warning: workflows/coproid.nf:261:32: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/coproid.nf:268:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

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