Nextflow lint results

Generated: 2026-03-04T00:20:50.383497918Z
Nextflow version: 26.02.0-edge
Summary: 17 errors, 31 warnings

❌ Errors

Error: main.nf:18:1: Included name 'BACTMAP' is not defined in module '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/bactmap/workflows/bactmap.nf'
```
include { BACTMAP                 } from './workflows/bactmap'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: main.nf:59:5: BACTMAP is not defined
```
    BACTMAP (
    ^^^^^^^
```

Error: main.nf:64:22: BACTMAP is not defined

    multiqc_report = BACTMAP.out.multiqc_report // channel: /path/to/multiqc_report.html
                     ^^^^^^^

Error: modules/local/alignpseudogenomes/main.nf:14:15: NUM_ALIGNMENT_GENOMES is not defined

    tuple env(NUM_ALIGNMENT_GENOMES), path("aligned_pseudogenomes.fas"), emit: aligned_pseudogenomes
              ^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/read_stats/main.nf:11:39: json is already declared

    tuple val(meta), path(json), path(json)
                                      ^^^^

Error: modules/nf-core/snpsites/main.nf:16:11: CONSTANT_SITES is not defined

    env   CONSTANT_SITES, emit: constant_sites_string
          ^^^^^^^^^^^^^^

Error: subworkflows/local/longread_adapterremoval/main.nf:17:9: Incorrect number of call arguments, expected 2 but received 1
```
        PORECHOP_ABI(reads)
        ^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/shortread_fastp/main.nf:23:22: reads is already declared

        .map { meta, reads -> [meta, reads, [] ] }
                     ^^^^^

Error: subworkflows/local/shortread_fastp/main.nf:25:22: reads is already declared

        .map { meta, reads -> [meta, reads, [] ] }
                     ^^^^^

Error: workflows/bactmap.nf:12:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

def checkPathParamList = [ params.input, params.fasta, params.multiqc_config,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/bactmap.nf:16:1: for loops are no longer supported

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
^^^

Error: workflows/bactmap.nf:16:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/bactmap.nf:16:6: param is not defined

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
     ^^^^^

Error: workflows/bactmap.nf:16:40: param is not defined

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
                                       ^^^^^^^

Error: workflows/bactmap.nf:16:55: param is not defined

for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
                                                      ^^^^^

Error: workflows/bactmap.nf:19:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if ( params.input ) {
^
```
Error: workflows/bactmap.nf:76:1: Invalid workflow definition -- check for missing or out-of-order section labels
```
workflow BACTMAP {
^
```

⚠️ Warnings

Warning: conf/modules.config:124:191: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) )  && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                              ^^

Warning: conf/modules.config:156:191: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs:  { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                              ^^

Warning: conf/modules.config:184:190: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                             ^^

Warning: conf/modules.config:214:225: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                ^^

Warning: conf/modules.config:228:190: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                             ^^

Warning: conf/modules.config:252:308: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                                                   ^^

Warning: conf/modules.config:276:304: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_longread_hostremoval && params.longread_qc_skipqualityfilter && !params.longread_qc_skipadaptertrim && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                                                               ^^

Warning: conf/modules.config:305:266: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                         ^^

Warning: conf/modules.config:334:266: Implicit closure parameter is deprecated, declare an explicit parameter instead

                saveAs: { (params.perform_runmerging == false || (params.perform_runmerging && !meta.is_multirun)) && !params.perform_longread_hostremoval && !params.longread_qc_skipqualityfilter && params.perform_longread_qc && params.save_analysis_ready_fastqs ? it : null },
                                                                                                                                                                                                                                                                         ^^

Warning: main.nf:50:20: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_fasta = Channel.fromPath(params.fasta, checkIfExists: true).collect()
                   ^^^^^^^

Warning: modules/local/bcftools/consensus/main.nf:46:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/bcftools/consensus/main.nf:48:9: Variable was declared but not used
```
    def masking = mask ? "-m $mask" : ""
        ^^^^^^^
```

Warning: modules/local/bedtools/genomecov/main.nf:30:9: Variable was declared but not used

    def buffer   = task.memory ? "--buffer-size=${task.memory.toGiga().intdiv(2)}G" : ''
        ^^^^^^

Warning: modules/local/clair3/main.nf:57:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/read_stats/main.nf:11:27: Variable was declared but not used
```
    tuple val(meta), path(json), path(json)
                          ^^^^
```

Warning: modules/nf-core/minimap2/align/main.nf:67:9: Variable was declared but not used

    def target = reference ?: (bam_input ? error("BAM input requires reference") : reads)
        ^^^^^^

Warning: modules/nf-core/nanoq/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/porechop/abi/main.nf:44:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/porechop/abi/main.nf:46:9: Variable was declared but not used

    def adapters_list = custom_adapters ? "--custom_adapters ${custom_adapters}" : ""
        ^^^^^^^^^^^^^

Warning: modules/nf-core/seqtk/comp/main.nf:32:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: subworkflows/local/bam_variant_calling_sort_freebayes_bcftools/main.nf:19:58: Parameter was not used -- prefix with _ to suppress warning

    FREEBAYES ( ch_input, ch_fasta_fai.map{ meta, fasta, fai -> [ meta, fasta ] }, ch_fasta_fai.map{ meta, fasta, fai -> [ meta, fai ] }, ch_samples, ch_populations, ch_cnv )
                                                         ^^^

Warning: subworkflows/local/bam_variant_calling_sort_freebayes_bcftools/main.nf:19:108: Parameter was not used -- prefix with _ to suppress warning

    FREEBAYES ( ch_input, ch_fasta_fai.map{ meta, fasta, fai -> [ meta, fasta ] }, ch_fasta_fai.map{ meta, fasta, fai -> [ meta, fai ] }, ch_samples, ch_populations, ch_cnv )
                                                                                                           ^^^^^

Warning: subworkflows/local/shortread_adapterremoval/main.nf:19:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        single: it[0].single_end
                ^^
```
Warning: subworkflows/local/shortread_adapterremoval/main.nf:20:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        paired: !it[0].single_end
                 ^^
```
Warning: subworkflows/local/shortread_fastp/main.nf:11:5: Parameter was not used -- prefix with _ to suppress warning
```
    adapterlist
    ^^^^^^^^^^^
```
Warning: subworkflows/local/shortread_fastp/main.nf:18:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        single: it[0]['single_end'] == true
                ^^
```
Warning: subworkflows/local/shortread_fastp/main.nf:19:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        paired: it[0]['single_end'] == false
                ^^
```
Warning: subworkflows/local/utils_nfcore_bactmap_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_bactmap_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/nf-core/fastq_align_bowtie2/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: workflows/bactmap.nf:20:5: Variable was declared but not used

    ch_input = file(params.input, checkIfExists: true)
    ^^^^^^^^

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