Nextflow lint results

Generated: 2026-02-18T00:22:42.332104795Z
Nextflow version: 26.01.1-edge
Summary: 42 warnings

⚠️ Warnings

Warning: conf/modules.config:187:23: Parameter was not used -- prefix with _ to suppress warning

            saveAs: { filename -> "${meta.id}_stardist_mask.tif" }
                      ^^^^^^^^

Warning: conf/modules.config:222:23: Parameter was not used -- prefix with _ to suppress warning

            saveAs: { filename -> "${meta.id}_cellpose_mask.tif" }
                      ^^^^^^^^

Warning: modules/nf-core/cellpose/main.nf:25:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

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

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/nf-core/stardist/main.nf:20:9: Variable was declared but not used

    def prefix             = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/nf-core/stardist/main.nf:38:9: Variable was declared but not used

    def args               = task.ext.args   ?: ''
        ^^^^

Warning: subworkflows/local/utils_nfcore_molkart_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_molkart_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_molkart_pipeline/main.nf:185:10: Variable was declared but not used
```
    def (meta, files) = input
         ^^^^
```
Warning: subworkflows/local/utils_nfcore_molkart_pipeline/main.nf:185:16: Variable was declared but not used
```
    def (meta, files) = input
               ^^^^^
```
Warning: workflows/molkart.nf:49:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[3] } // filter samples with membrane
                  ^^
```

Warning: workflows/molkart.nf:87:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

            def sorted = [tiffs, stains].transpose().sort { it[1] }
                                                            ^^

Warning: workflows/molkart.nf:94:33: Implicit closure parameter is deprecated, declare an explicit parameter instead

    grouped_map_stack.filter { !it[2] } // for rows without a present membrane image, set channel to no_stack
                                ^^

Warning: workflows/molkart.nf:97:31: Implicit closure parameter is deprecated, declare an explicit parameter instead

    grouped_map_stack.filter{ it[2] }      // for rows where the membrane image is present, create a list of images to be stacked
                              ^^

Warning: workflows/molkart.nf:104:10: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        [it[0], it[1]]
         ^^
```
Warning: workflows/molkart.nf:104:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        [it[0], it[1]]
                ^^
```
Warning: workflows/molkart.nf:118:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it[2] == null ? tuple(it[0], 1) : tuple(it[0], 2)
                ^^
```

Warning: workflows/molkart.nf:118:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it[2] == null ? tuple(it[0], 1) : tuple(it[0], 2)
                                      ^^

Warning: workflows/molkart.nf:118:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it[2] == null ? tuple(it[0], 1) : tuple(it[0], 2)
                                                        ^^

Warning: workflows/molkart.nf:129:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    tuple('matchkey', it[1])
                                      ^^
```
Warning: workflows/molkart.nf:130:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    }.groupTuple().map{ it[1]} )
                                        ^^
```
Warning: workflows/molkart.nf:148:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            grouped_map_stack.map{ tuple(it[0], it[1]) },
                                         ^^
```

Warning: workflows/molkart.nf:148:49: Implicit closure parameter is deprecated, declare an explicit parameter instead

            grouped_map_stack.map{ tuple(it[0], it[1]) },
                                                ^^

Warning: workflows/molkart.nf:150:17: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it[2] == null ? [[:],[]] : tuple(it[0], it[2]) // if no membrane channel specified, give empty membrane input; if membrane image exists, provide it to the process
                ^^

Warning: workflows/molkart.nf:150:50: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it[2] == null ? [[:],[]] : tuple(it[0], it[2]) // if no membrane channel specified, give empty membrane input; if membrane image exists, provide it to the process
                                                 ^^

Warning: workflows/molkart.nf:150:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it[2] == null ? [[:],[]] : tuple(it[0], it[2]) // if no membrane channel specified, give empty membrane input; if membrane image exists, provide it to the process
                                                        ^^

Warning: workflows/molkart.nf:177:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

            cellpose_custom_model ? cellpose_custom_model.map{it[2]} : []
                                                              ^^

Warning: workflows/molkart.nf:193:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                it[2] == null ? tuple(it[0], 1) : tuple(it[0], 2)
                ^^
```

Warning: workflows/molkart.nf:193:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it[2] == null ? tuple(it[0], 1) : tuple(it[0], 2)
                                      ^^

Warning: workflows/molkart.nf:193:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it[2] == null ? tuple(it[0], 1) : tuple(it[0], 2)
                                                        ^^

Warning: workflows/molkart.nf:203:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ilastik_in.map{ [it[0], it[1]] },
                             ^^
```
Warning: workflows/molkart.nf:203:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ilastik_in.map{ [it[0], it[1]] },
                                    ^^
```
Warning: workflows/molkart.nf:204:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ilastik_in.map{ [it[0], it[2]] }
                             ^^
```
Warning: workflows/molkart.nf:204:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ilastik_in.map{ [it[0], it[2]] }
                                    ^^
```
Warning: workflows/molkart.nf:216:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multicut_in.map{ tuple(it[0], it[1]) },
                                   ^^
```
Warning: workflows/molkart.nf:216:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multicut_in.map{ tuple(it[0], it[1]) },
                                          ^^
```
Warning: workflows/molkart.nf:217:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multicut_in.map{ tuple(it[0], it[4]) },
                                   ^^
```
Warning: workflows/molkart.nf:217:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multicut_in.map{ tuple(it[0], it[4]) },
                                          ^^
```
Warning: workflows/molkart.nf:218:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multicut_in.map{ tuple(it[0], it[3]) }
                                   ^^
```
Warning: workflows/molkart.nf:218:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multicut_in.map{ tuple(it[0], it[3]) }
                                          ^^
```
Warning: workflows/molkart.nf:348:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            CROPHDF5.out.crop_summary.map{it[1]}
                                          ^^
```
Warning: workflows/molkart.nf:353:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            MOLKARTQC.out.qc.map{it[1]}
                                 ^^
```

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nextflow lint results

⚠️ Warnings

FilesExpand file tree

molkart_lint.md

Latest commit

History

molkart_lint.md

File metadata and controls

Nextflow lint results

⚠️ Warnings