Nextflow lint results

Generated: 2026-01-16T10:20:19.506365889Z
Nextflow version: 25.12.0-edge
Summary: 2 errors, 48 warnings

❌ Errors

Error: conf/modules.config:83:17: Unexpected input: ':'

        withName: 'NFCORE_DUALRNASEQ:DUALRNASEQ:SALMON_SELECTIVE_ALIGNMENT:SALMON_INDEX' {
                ^

Error: nextflow.config:462:14: Unexpected input: '('
```
def check_max(obj, type) {
             ^
```

⚠️ Warnings

Warning: modules/local/combine_files/main.nf:14:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/combine_quantification_results_salmon/main.nf:15:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/salmon_split_table/main.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/tximport/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/tximport/main.nf:22:5: Variable was declared but not used
```
    prefix = task.ext.prefix ?: "${meta.id}"
    ^^^^^^
```
Warning: modules/nf-core/custom/dumpsoftwareversions/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/prepare_pathogen_transcriptome/main.nf:12:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    parameters = Channel.value(
                 ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:58:43: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_combined_pathogen_host_gff_htseq = Channel.empty()
                                          ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:59:43: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_extracted_annotations_host_htseq = Channel.empty()
                                          ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:60:45: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_extract_annotations_pathogen_htseq = Channel.empty()
                                            ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:61:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_combined_fasta_transcripts = Channel.empty()
                                    ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:62:42: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_host_fasta_transcripts_unzipped = Channel.empty()
                                         ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:63:46: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_pathogen_fasta_transcripts_unzipped = Channel.empty()
                                             ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:77:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gene_feature_pathogen = Channel.value(pathogenFeaturesList)
                               ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:83:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gene_feature_host = Channel.value(hostFeaturesList)
                           ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:93:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_host_fasta_genome = Channel.value(file(host_fasta_genome, checkIfExists: true))
                           ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:94:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_host_gff = Channel.value(file(host_gff, checkIfExists: true))
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:95:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_pathogen_gff = Channel.value(file(pathogen_gff, checkIfExists: true))
                      ^^^^^^^
```
Warning: subworkflows/local/prepare_reference_files/main.nf:96:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_pathogen_fasta_genome = Channel.value(file(pathogen_fasta_genome, checkIfExists: true))
                               ^^^^^^^
```

Warning: subworkflows/local/prepare_reference_files/main.nf:157:73: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_host_fasta_transcripts = params.host_fasta_transcripts ? Channel.value(file(params.host_fasta_transcripts, checkIfExists: true)) : Channel.empty()
                                                                        ^^^^^^^

Warning: subworkflows/local/prepare_reference_files/main.nf:157:147: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_host_fasta_transcripts = params.host_fasta_transcripts ? Channel.value(file(params.host_fasta_transcripts, checkIfExists: true)) : Channel.empty()
                                                                                                                                                  ^^^^^^^

Warning: subworkflows/local/prepare_reference_files/main.nf:181:81: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_pathogen_fasta_transcripts = params.pathogen_fasta_transcripts ? Channel.value(file(params.pathogen_fasta_transcripts, checkIfExists: true)) : Channel.empty()
                                                                                ^^^^^^^

Warning: subworkflows/local/prepare_reference_files/main.nf:181:159: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_pathogen_fasta_transcripts = params.pathogen_fasta_transcripts ? Channel.value(file(params.pathogen_fasta_transcripts, checkIfExists: true)) : Channel.empty()
                                                                                                                                                              ^^^^^^^

Warning: subworkflows/local/prepare_reference_files/main.nf:383:116: The use of Channel to access channel factories is deprecated -- use channel instead

    host_pathogen_transcripts_gff   = params.salmon_sa || params.salmon_ab ? COMBINE_FILES_PATHOGEN_HOST_GFF.out : Channel.empty() // 'host_pathogen_transcripts.gff'
                                                                                                                   ^^^^^^^

Warning: subworkflows/local/prepare_reference_files/main.nf:384:128: The use of Channel to access channel factories is deprecated -- use channel instead

    annotations_host_salmon         = params.salmon_sa || params.salmon_ab ? EXTRACT_ANNOTATIONS_HOST_SALMON.out.annotations : Channel.empty() // extracted_annotations_host_salmon.tsv
                                                                                                                               ^^^^^^^

Warning: subworkflows/local/prepare_reference_files/main.nf:385:132: The use of Channel to access channel factories is deprecated -- use channel instead

    annotations_pathogen_salmon     = params.salmon_sa || params.salmon_ab ? EXTRACT_ANNOTATIONS_PATHOGEN_SALMON.out.annotations : Channel.empty() // extracted_annotations_pathogen_salmon.tsv
                                                                                                                                   ^^^^^^^

Warning: subworkflows/local/salmon_alignment_based/main.nf:24:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/salmon_alignment_based/main.nf:82:50: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    input_files = SALMON_QUANT.out.results.map { it[1] }.collect()
                                                 ^^
```
Warning: subworkflows/local/salmon_alignment_based/main.nf:87:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.value("both"),
        ^^^^^^^
```
Warning: subworkflows/local/salmon_alignment_based/main.nf:96:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: "combined"], [it]] }
                                   ^^
```
Warning: subworkflows/local/salmon_selective_alignment/main.nf:21:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/salmon_selective_alignment/main.nf:64:50: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    input_files = SALMON_QUANT.out.results.map { it[1] }.collect()
                                                 ^^
```
Warning: subworkflows/local/salmon_selective_alignment/main.nf:69:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.value("both"),
        ^^^^^^^
```
Warning: subworkflows/local/salmon_selective_alignment/main.nf:78:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: "combined"], [it]] }
                                   ^^
```
Warning: subworkflows/local/star_htseq/main.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_dualrnaseq_pipeline/main.nf:30:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_dualrnaseq_pipeline/main.nf:33:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_dualrnaseq_pipeline/main.nf:37:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_dualrnaseq_pipeline/main.nf:74:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
    ^^^^^^^
```

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/dualrnaseq.nf:44:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/dualrnaseq.nf:45:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/dualrnaseq.nf:50:25: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_config = Channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
                        ^^^^^^^

Warning: workflows/dualrnaseq.nf:51:56: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
                                                       ^^^^^^^

Warning: workflows/dualrnaseq.nf:51:98: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty()
                                                                                                 ^^^^^^^

Warning: workflows/dualrnaseq.nf:52:45: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo) : Channel.empty()
                                            ^^^^^^^

Warning: workflows/dualrnaseq.nf:52:85: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo) : Channel.empty()
                                                                                    ^^^^^^^

Warning: workflows/dualrnaseq.nf:61:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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