Nextflow lint results

Generated: 2026-03-06T00:24:13.355399741Z
Nextflow version: 26.02.0-edge
Summary: 43 warnings

⚠️ Warnings

Warning: modules/local/mat2json/main.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mat2json/main.nf:42:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorph3dunet/main.nf:48:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphalign/main.nf:29:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphalign/main.nf:59:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphintensity/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphintensity/main.nf:46:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphregister/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphregister/main.nf:48:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphresample/main.nf:18:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphresample/main.nf:19:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/numorphresample/main.nf:40:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphstitch/main.nf:26:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/numorphstitch/main.nf:77:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/stagefiles/main.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/stagefiles/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/stagefiles/main.nf:42:9: Variable was declared but not used

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

Warning: modules/nf-core/unzip/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/araregistration/main.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/araregistration/main.nf:15:45: Parameter was not used -- prefix with _ to suppress warning

    sample_meta = stitched_data.map { meta, img_dir, params -> meta }
                                            ^^^^^^^

Warning: subworkflows/local/araregistration/main.nf:15:54: Parameter was not used -- prefix with _ to suppress warning

    sample_meta = stitched_data.map { meta, img_dir, params -> meta }
                                                     ^^^^^^

Warning: subworkflows/local/araregistration/main.nf:27:33: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, resampled, stitched_img_directory, parameter_file ->
                                ^^^^^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/numorph_preprocessing/main.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/numorph_preprocessing/main.nf:19:43: Parameter was not used -- prefix with _ to suppress warning

    sample_meta = samplesheet.map { meta, img_dir, params -> meta }
                                          ^^^^^^^

Warning: subworkflows/local/numorph_preprocessing/main.nf:19:52: Parameter was not used -- prefix with _ to suppress warning

    sample_meta = samplesheet.map { meta, img_dir, params -> meta }
                                                   ^^^^^^

Warning: subworkflows/local/numorph_stitch/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/numorph_stitch/main.nf:18:43: Parameter was not used -- prefix with _ to suppress warning

    sample_meta = samplesheet.map { meta, img_dir, params -> meta }
                                          ^^^^^^^

Warning: subworkflows/local/numorph_stitch/main.nf:18:52: Parameter was not used -- prefix with _ to suppress warning

    sample_meta = samplesheet.map { meta, img_dir, params -> meta }
                                                   ^^^^^^

Warning: subworkflows/local/utils_nfcore_lsmquant_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_lsmquant_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_lsmquant_pipeline/main.nf:103:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samplesheet = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
                     ^^^^^^^
```
Warning: workflows/lsmquant.nf:35:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/lsmquant.nf:36:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/lsmquant.nf:50:27: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, zip, parameter_file ->
                          ^^^^^^^^^^^^^^

Warning: workflows/lsmquant.nf:61:32: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, unzipped, zip, parameter_file ->
                               ^^^

Warning: workflows/lsmquant.nf:68:37: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, img_directory, parameter_file ->
                                    ^^^^^^^^^^^^^^

Warning: workflows/lsmquant.nf:79:30: Parameter was not used -- prefix with _ to suppress warning

        .map { meta, staged, raw_img_directory, parameter_file ->
                             ^^^^^^^^^^^^^^^^^

Warning: workflows/lsmquant.nf:85:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samplesheet = Channel.empty()
                     ^^^^^^^
```

Warning: workflows/lsmquant.nf:114:36: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, stitched, raw_img_directory, parameter_file ->
                                   ^^^^^^^^^^^^^^^^^

Warning: workflows/lsmquant.nf:129:36: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, stitched, raw_img_directory, parameter_file ->
                                   ^^^^^^^^^^^^^^^^^

Warning: workflows/lsmquant.nf:144:36: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, stitched, raw_img_directory, parameter_file ->
                                   ^^^^^^^^^^^^^^^^^

Warning: workflows/lsmquant.nf:152:22: The use of Channel to access channel factories is deprecated -- use channel instead

        model_file = Channel.fromPath(params.model_file, checkIfExists: !params.model_file.startsWith('http'))
                     ^^^^^^^

Warning: workflows/lsmquant.nf:165:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def topic_versions = Channel.topic("versions")
                         ^^^^^^^
```

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