Nextflow lint results

Generated: 2026-01-16T10:19:14.049777445Z
Nextflow version: 25.12.0-edge
Summary: 10 errors, 49 warnings

❌ Errors

Error: conf/modules.config:100:9: If statements cannot be mixed with config statements
```
        if (params.container_dev) {
        ^
```
Error: conf/modules.config:111:9: If statements cannot be mixed with config statements
```
        if (params.container_dev) {
        ^
```
Error: conf/modules.config:125:9: If statements cannot be mixed with config statements
```
        if (params.container_dev) {
        ^
```
Error: conf/modules.config:136:9: If statements cannot be mixed with config statements
```
        if (params.container_dev) {
        ^
```
Error: conf/modules.config:152:9: If statements cannot be mixed with config statements
```
        if (params.container_dev) {
        ^
```
Error: conf/modules.config:160:9: If statements cannot be mixed with config statements
```
        if (params.container_dev) {
        ^
```
Error: conf/modules.config:167:9: If statements cannot be mixed with config statements
```
        if (params.container_dev) {
        ^
```

Error: modules/local/bedtools/random/main.nf:15:27: Unexpected input: '"*.bed"'

    tuple val(meta), path "*.bed", emit: bed
                          ^

Error: modules/local/stimulus/check_model/main.nf:3:12: meta is not defined
```
    tag "${meta.id}"
           ^^^^
```
Error: nextflow.config:214:5: Unexpected input: 'includeConfig'
```
    includeConfig 'conf/igenomes.config'
    ^
```

⚠️ Warnings

Warning: modules/local/stimulus/tune/main.nf:22:9: Variable was declared but not used

    def use_initial_weights = initial_weights != [] ? "-w ${initial_weights}" : ""
        ^^^^^^^^^^^^^^^^^^^

Warning: modules/nf-core/custom/getchromsizes/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/gawk/main.nf:25:51: Implicit closure parameter is deprecated, declare an explicit parameter instead

    suffix = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files
                                                  ^^

Warning: modules/nf-core/gawk/main.nf:28:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    lst_gz    = input.collect{ it.getExtension().endsWith("gz") }
                               ^^
```

Warning: modules/nf-core/gawk/main.nf:34:16: Implicit closure parameter is deprecated, declare an explicit parameter instead

        assert it.name != "${prefix}.${suffix}" : "Input and output names are the same, set prefix in module configuration to disambiguate!"
               ^^

Warning: subworkflows/local/check_model/main.nf:26:5: Variable was declared but not used
```
    ch_versions = Channel.empty()
    ^^^^^^^^^^^
```
Warning: subworkflows/local/check_model/main.nf:26:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/evaluation/main.nf:25:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/evaluation/main.nf:75:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .flatMap { it }
                   ^^
```
Warning: subworkflows/local/evaluation/main.nf:85:9: Parameter was not used -- prefix with _ to suppress warning
```
        meta, csv -> csv
        ^^^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:51:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:61:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .combine(ch_genome_sizes.map{it[1]})
                                     ^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:65:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_awk_program = Channel.fromPath('./bin/center_around_peak.sh')
                     ^^^^^^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:102:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it.background_type == 'aliens' }
                  ^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:126:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            shade: it[0].background_type == 'shade'
                   ^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:127:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            shuffle: it[0].background_type == 'shuffle'
                     ^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:185:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_genome.map{it[1]}.collect()
                      ^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:191:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_genome.map{it[1]}.collect()
                      ^^
```
Warning: subworkflows/local/preprocess_ibis_bedfile_to_stimulus/main.nf:210:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_awk_program = Channel.fromPath('./bin/background_foreground_to_stimulus_csv.sh')
                     ^^^^^^^
```
Warning: subworkflows/local/split_csv/main.nf:23:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/split_data_config_unified/main.nf:21:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/transform_csv/main.nf:25:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/tune/main.nf:28:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/tune/main.nf:56:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .combine(ch_model.map{it[1]})
                              ^^
```

Warning: subworkflows/local/tune/main.nf:60:73: Parameter was not used -- prefix with _ to suppress warning

        .multiMap { meta, data, model, meta_model_config, model_config, meta_weights, initial_weights, n_replicate ->
                                                                        ^^^^^^^^^^^^

Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:31:5: Parameter was not used -- prefix with _ to suppress warning
```
    monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:39:5: Parameter was not used -- prefix with _ to suppress warning
```
    preprocessing_config
    ^^^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:43:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:74:26: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_data            = Channel.fromPath(data, checkIfExists: true).map { it -> [[id:it.baseName], it]}
                         ^^^^^^^

Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:75:26: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_data_config     = Channel.fromPath(data_config, checkIfExists: true).map { it -> [[id:it.baseName], it]}
                         ^^^^^^^

Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:76:26: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_model           = Channel.fromPath(model, checkIfExists: true).map { it -> [[id:it.baseName], it]}
                         ^^^^^^^

Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:77:26: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_model_config    = Channel.fromPath(model_config, checkIfExists: true).map { it -> [[id:it.baseName], it]}
                         ^^^^^^^

Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:83:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.of([[],[]]) :
        ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:84:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(initial_weights, checkIfExists: true)
        ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:92:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty() :
        ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:93:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromList(samplesheetToList(params.preprocessing_config, "assets/schema_preprocessing.json")).map{it[0]}
        ^^^^^^^
```

Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:93:114: Implicit closure parameter is deprecated, declare an explicit parameter instead

        Channel.fromList(samplesheetToList(params.preprocessing_config, "assets/schema_preprocessing.json")).map{it[0]}
                                                                                                                 ^^

Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:99:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.of([[],[]]) :
        ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:102:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.genomes[params.genome]['fasta'], checkIfExists: true) :
            ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:103:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.genome, checkIfExists: true)
            ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:114:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
        val_tune_trials_range = Channel.from(range)
                                ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:126:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_tune_replicates = Channel.from(1..params.tune_replicates)
                         ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:132:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty() :
            ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_deepmodeloptim_pipeline/main.nf:133:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.prediction_data, checkIfExists: true)
            ^^^^^^^
```

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/deepmodeloptim.nf:48:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: workflows/deepmodeloptim.nf:65:44: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_preprocessing_config.filter{it.protocol == 'ibis'},
                                           ^^

Warning: workflows/deepmodeloptim.nf:127:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter{it}   // remove the empty element from the check model
                ^^
```

Warning: workflows/deepmodeloptim.nf:160:17: Variable was declared but not used

        ).set { ch_collated_versions }
                ^^^^^^^^^^^^^^^^^^^^

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