Nextflow lint results

Generated: 2026-02-23T00:22:00.522865043Z
Nextflow version: 26.01.1-edge
Summary: 8 errors, 45 warnings

❌ Errors

Error: modules/local/create_anndata_mudata/main.nf:34:9: prefix is already declared

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

Error: modules/local/extract_hashes/main.nf:33:9: prefix is already declared

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

Error: modules/local/gene_summary/main.nf:34:9: prefix is already declared

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

Error: modules/local/hash_summary/main.nf:39:9: prefix is already declared

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

Error: modules/local/htodemux_visualization/main.nf:59:9: prefix is already declared

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

Error: modules/local/preprocessing_for_htodemux_multiseq/main.nf:38:9: prefix is already declared
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```

Error: modules/nf-core/demuxem/main.nf:51:9: prefix is already declared

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

Error: subworkflows/local/hash_demultiplexing/main.nf:115:57: gmmdemux_estimated_n_cells is not defined

                    params.gmmdemux_estimated_n_cells ? gmmdemux_estimated_n_cells : [],
                                                        ^^^^^^^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/create_anndata_mudata/main.nf:29:5: Variable was declared but not used
```
    prefix = task.ext.prefix ?: "${meta.id}"
    ^^^^^^
```
Warning: modules/local/gene_summary/main.nf:29:5: Variable was declared but not used
```
    prefix = task.ext.prefix ?: "${meta.id}"
    ^^^^^^
```

Warning: modules/local/hash_summary/main.nf:33:5: Variable was declared but not used

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

Warning: modules/local/hash_summary/main.nf:34:5: Variable was declared but not used
```
    hash_list      = "${meta.hto_names}".split(",")
    ^^^^^^^^^
```

Warning: modules/local/htodemux_visualization/main.nf:27:5: Variable was declared but not used

    ridgePlot      = task.ext.ridgePlot      ?: true         // Generate ridge plot
    ^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:28:5: Variable was declared but not used

    ridgeNCol      = task.ext.ridgeNCol      ?: 2            // Number of columns for ridge plot
    ^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:31:5: Variable was declared but not used

    featureScatter = task.ext.featureScatter ?: true         // Generate feature scatter plot
    ^^^^^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:32:5: Variable was declared but not used

    scatterFeat1   = task.ext.scatterFeat1   ?: null         // Feature 1 for scatter plot
    ^^^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:33:5: Variable was declared but not used

    scatterFeat2   = task.ext.scatterFeat2   ?: null         // Feature 2 for scatter plot
    ^^^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:36:5: Variable was declared but not used

    vlnPlot        = task.ext.vlnPlot        ?: true         // Generate violin plot
    ^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:37:5: Variable was declared but not used

    vlnFeatures    = task.ext.vlnFeatures    ?: "nCount_RNA" // Features to plot (gene expression, metrics, PC scores, anything that can be retreived by FetchData)
    ^^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:38:5: Variable was declared but not used

    vlnLog         = task.ext.vlnLog         ?: true         // Plot the feature axis on log scale
    ^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:41:5: Variable was declared but not used

    tSNE           = task.ext.tSNE           ?: true         // Generate a two dimensional tSNE embedding for HTOs
    ^^^^

Warning: modules/local/htodemux_visualization/main.nf:42:5: Variable was declared but not used

    tSNEIdents     = task.ext.tSNEIdents     ?: "Negative"   // What should we remove from the object (we have Singlet,Doublet and Negative)
    ^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:43:5: Variable was declared but not used

    tSNEInvert     = task.ext.tSNEInvert     ?: true         // Invert tSNE selection
    ^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:44:5: Variable was declared but not used

    tSNEVerbose    = task.ext.tSNEVerbose    ?: false        // Verbose tSNE
    ^^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:45:5: Variable was declared but not used

    tSNEApprox     = task.ext.tSNEApprox     ?: false        // Approximate tSNE
    ^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:46:5: Variable was declared but not used

    tSNEDimMax     = task.ext.tSNEDimMax     ?: 2            // Max number of donors
    ^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:47:5: Variable was declared but not used

    tSNEPerplexity = task.ext.tSNEPerplexity ?: 100          // Value for perplexity
    ^^^^^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:50:5: Variable was declared but not used

    heatMap        = task.ext.heatMap        ?: true         // Generate heatmap
    ^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:51:5: Variable was declared but not used

    heatMapNcells  = task.ext.heatMapNcells  ?: 500          // Number of cells for heatmap
    ^^^^^^^^^^^^^

Warning: modules/local/htodemux_visualization/main.nf:54:5: Variable was declared but not used

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

Warning: modules/local/preprocessing_for_htodemux_multiseq/main.nf:24:5: Variable was declared but not used

    sel_method  = task.ext.sel_method  ?: "mean.var.plot" // Selection method
    ^^^^^^^^^^

Warning: modules/local/preprocessing_for_htodemux_multiseq/main.nf:25:5: Variable was declared but not used

    ndelim      = task.ext.ndelim      ?: "_"             // For the initial identity class for each cell, delimiter for the cell's column name
    ^^^^^^

Warning: modules/local/preprocessing_for_htodemux_multiseq/main.nf:26:5: Variable was declared but not used

    n_features  = task.ext.n_features  ?: 2000            // Number of features to be used when finding variable features
    ^^^^^^^^^^

Warning: modules/local/preprocessing_for_htodemux_multiseq/main.nf:27:5: Variable was declared but not used

    assay       = task.ext.assay       ?: "HTO"           // Assay name for hashing modality
    ^^^^^

Warning: modules/local/preprocessing_for_htodemux_multiseq/main.nf:28:5: Variable was declared but not used

    margin      = task.ext.margin      ?: 2               // Margin for normalisation
    ^^^^^^

Warning: modules/local/preprocessing_for_htodemux_multiseq/main.nf:29:5: Variable was declared but not used

    norm_method = task.ext.norm_method ?: "CLR"           // Normalisation method
    ^^^^^^^^^^^

Warning: modules/local/preprocessing_for_htodemux_multiseq/main.nf:30:5: Variable was declared but not used

    gene_col    = task.ext.gene_col    ?: 2               // Specify which column of genes.tsv or features.tsv to use for gene names
    ^^^^^^^^

Warning: modules/local/preprocessing_for_htodemux_multiseq/main.nf:33:5: Variable was declared but not used
```
    prefix      = task.ext.prefix      ?: "${meta.id}"
    ^^^^^^
```

Warning: modules/nf-core/gmmdemux/main.nf:62:9: Variable was declared but not used

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

Warning: subworkflows/local/genetic_demultiplexing/main.nf:134:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { tuple -> tuple.collect { it == null ? [] : it } }
                                        ^^
```
Warning: subworkflows/local/genetic_demultiplexing/main.nf:134:59: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { tuple -> tuple.collect { it == null ? [] : it } }
                                                          ^^
```
Warning: subworkflows/local/hash_demultiplexing/main.nf:51:13: Variable was declared but not used
```
            ch_assignments = HTODEMUX.out.assignment
            ^^^^^^^^^^^^^^
```

Warning: subworkflows/local/hash_demultiplexing/main.nf:56:13: Variable was declared but not used

            ch_classifications = HTODEMUX.out.classification
            ^^^^^^^^^^^^^^^^^^

Warning: subworkflows/local/hash_demultiplexing/main.nf:162:45: Parameter was not used -- prefix with _ to suppress warning

    ch_summary = ch_samplesheet.map { meta, rna, hto -> [meta,hto] }
                                            ^^^

Warning: subworkflows/local/hash_demultiplexing/main.nf:173:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { tuple -> tuple.collect { it == null ? [] : it } }
                                        ^^
```
Warning: subworkflows/local/hash_demultiplexing/main.nf:173:59: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { tuple -> tuple.collect { it == null ? [] : it } }
                                                          ^^
```
Warning: subworkflows/local/utils_nfcore_hadge_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_hadge_pipeline/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_hadge_pipeline/main.nf:217:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    if(meta.hto_names.split(",").any { it.contains('_') }){
                                       ^^
```

Warning: subworkflows/local/utils_nfcore_hadge_pipeline/main.nf:218:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def bad = meta.hto_names.split(",").findAll { it.contains('_') }.join(', ')
                                                      ^^

Warning: workflows/hadge.nf:84:46: Parameter was not used -- prefix with _ to suppress warning

    ch_genetic = ch_preprocessed.map { meta, rna, _hto, bam, barcodes, vcf -> [meta, bam, barcodes, vcf] }
                                             ^^^

Warning: workflows/hadge.nf:194:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

                if (params.mode == 'genetic'){ tuple.collect { it == null ? [] : it } }
                                                               ^^

Warning: workflows/hadge.nf:194:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

                if (params.mode == 'genetic'){ tuple.collect { it == null ? [] : it } }
                                                                                 ^^

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