Nextflow lint results

Generated: 2026-02-05T00:21:47.459011877Z
Nextflow version: 25.12.0-edge
Summary: 6 errors, 35 warnings

❌ Errors

Error: nextflow.config:293:36: manifest is not defined

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

Error: nextflow.config:296:26: 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:296:69: 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:296:186: 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:305:22: validation is not defined

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

Error: nextflow.config:306:21: validation is not defined

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

⚠️ Warnings

Warning: modules/local/cellprofiler/analysis.nf:77:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/cellprofiler/assaydevelopment.nf:27:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/cellprofiler/assaydevelopment.nf:28:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/cellprofiler/assaydevelopment.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/cellprofiler/illuminationcorrection/main.nf:24:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/cellprofiler/illuminationcorrection/main.nf:45:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/cellprofiler/illuminationcorrection/main.nf:46:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```

Warning: nextflow.config:296:129: 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/cellprofiler_load_data_csv/main.nf:20:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            def group_id = keys.collect { meta[it] }.join('_')
                                              ^^
```

Warning: subworkflows/local/cellprofiler_load_data_csv/main.nf:31:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def image_channels = meta_list.collect { it.channel }.unique().sort()
                                                     ^^

Warning: subworkflows/local/cellprofiler_load_data_csv/main.nf:38:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            }.groupBy { it[0] }
                        ^^
```

Warning: subworkflows/local/cellprofiler_load_data_csv/main.nf:43:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def row_channels = entries.collect { it[1] }  // Extract channels
                                                     ^^

Warning: subworkflows/local/cellprofiler_load_data_csv/main.nf:44:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def row_images = entries.collect { it[2] }    // Extract images
                                                   ^^

Warning: subworkflows/local/cellprofiler_load_data_csv_with_illum/main.nf:19:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def group_meta = meta.subMap(grouping_keys) + [id: grouping_keys.collect { meta[it] }.join('_')]
                                                                                           ^^

Warning: subworkflows/local/cellprofiler_load_data_csv_with_illum/main.nf:29:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            def channels = meta_list.collect { it.channel }.unique().sort()
                                               ^^
```
Warning: subworkflows/local/cellprofiler_load_data_csv_with_illum/main.nf:42:67: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            def orig_headers = channels.collect { "FileName_Orig${it}" }
                                                                  ^^
```

Warning: subworkflows/local/cellprofiler_load_data_csv_with_illum/main.nf:43:69: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def illum_headers = channels.collect { "FileName_Illum${it}" }
                                                                    ^^

Warning: subworkflows/local/cellprofiler_load_data_csv_with_illum/main.nf:94:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def illum_grouping_keys = grouping_keys.findAll { illum_meta.containsKey(it) }
                                                                                     ^^

Warning: subworkflows/local/cellprofiler_load_data_csv_with_illum/main.nf:95:116: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def group_meta = illum_meta.subMap(illum_grouping_keys) + [id: illum_grouping_keys.collect { illum_meta[it] }.join('_')]
                                                                                                                   ^^

Warning: subworkflows/local/cellprofiler_load_data_csv_with_illum/main.nf:111:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def illum_keys = ['batch', 'plate'].findAll { first_meta.containsKey(it) }
                                                                                 ^^

Warning: subworkflows/local/cellprofiler_load_data_csv_with_illum/main.nf:112:60: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            def illum_key = illum_keys.collect { first_meta[it] }.join('_')
                                                           ^^
```
Warning: subworkflows/local/utils_nfcore_cellpainting_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_cellpainting_pipeline/main.nf:38:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_cellpainting_pipeline/main.nf:70:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```

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/cellpainting.nf:32:5: Parameter was not used -- prefix with _ to suppress warning

    cellprofiler_analysis_cppipe // value: path to analysis cppipe
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/cellpainting.nf:37:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/cellpainting.nf:38:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/cellpainting.nf:93:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/cellpainting.nf:96:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/cellpainting.nf:97:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/cellpainting.nf:99:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/cellpainting.nf:100:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/cellpainting.nf:104:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                          ^^^^^^^
```

Warning: workflows/cellpainting.nf:110:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nextflow lint results

❌ Errors

⚠️ Warnings

FilesExpand file tree

cellpainting_lint.md

Latest commit

History

cellpainting_lint.md

File metadata and controls

Nextflow lint results

❌ Errors

⚠️ Warnings