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Nextflow lint results

  • Generated: 2026-06-07T00:43:12.637530075Z
  • Nextflow version: 26.04.3
  • Summary: 30 warnings

⚠️ Warnings

  • Warning: main.nf:145:5: Emit name should be omitted when there is only one emit

        multiqc_report = SCDOWNSTREAM.out.multiqc_report // channel: /path/to/multiqc_report.html
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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

        force_obs_cols = task.ext.force_obs_cols ?: params.force_obs_cols ?: ""
    ^^^^^^^^^^^^^^

  • Warning: modules/local/adata/mygene/main.nf:23:5: Variable was declared but not used

        input_col = task.ext.input_col ?: "index"
    ^^^^^^^^^

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

        output_col = task.ext.output_col ?: "symbols"
    ^^^^^^^^^^

  • Warning: modules/local/liana/rankaggregate/main.nf:22:5: Variable was declared but not used

        obs_key = meta.obs_key ?: "leiden"
    ^^^^^^^

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

        batch_key = task.ext.batch_key ?: ""
    ^^^^^^^^^

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

        obs_key = meta.obs_key ?: "leiden"
    ^^^^^^^

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

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

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

        n_hidden = task.ext.n_hidden ?: 128
    ^^^^^^^^

  • Warning: modules/local/scvitools/scanvi/main.nf:34:5: Variable was declared but not used

        n_layers = task.ext.n_layers ?: 2
    ^^^^^^^^

  • Warning: modules/local/scvitools/scanvi/main.nf:35:5: Variable was declared but not used

        n_latent = task.ext.n_latent ?: 30
    ^^^^^^^^

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

        dispersion = task.ext.dispersion ?: 'gene'
    ^^^^^^^^^^

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

        gene_likelihood = task.ext.gene_likelihood ?: 'zinb'
    ^^^^^^^^^^^^^^^

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

        max_epochs = task.ext.max_epochs ?: null
    ^^^^^^^^^^

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

        n_hidden = task.ext.n_hidden ?: 128
    ^^^^^^^^

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

        n_layers = task.ext.n_layers ?: 2
    ^^^^^^^^

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

        n_latent = task.ext.n_latent ?: 30
    ^^^^^^^^

  • Warning: modules/local/scvitools/scvi/main.nf:34:5: Variable was declared but not used

        dispersion = task.ext.dispersion ?: 'gene'
    ^^^^^^^^^^

  • Warning: modules/local/scvitools/scvi/main.nf:35:5: Variable was declared but not used

        gene_likelihood = task.ext.gene_likelihood ?: 'zinb'
    ^^^^^^^^^^^^^^^

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

        max_epochs = task.ext.max_epochs ?: null
    ^^^^^^^^^^

  • Warning: subworkflows/local/ambient_correction/main.nf:111:5: Emit name should be omitted when there is only one emit

        h5ad     = ch_h5ad     // channel: [ meta, h5ad ]
    ^^^^^^^^^^^^

  • Warning: subworkflows/local/celltype_assignment/main.nf:39:5: Emit name should be omitted when there is only one emit

        obs      = ch_obs      // channel: [ meta, pkl ]
    ^^^^^^^^^^

  • Warning: subworkflows/local/load_h5ad/main.nf:75:5: Emit name should be omitted when there is only one emit

        h5ad     = ch_output   // channel: [ meta, h5ad, h5ad ]
    ^^^^^^^^^^^^^^

  • Warning: subworkflows/local/pseudobulking/main.nf:22:5: Emit name should be omitted when there is only one emit

        h5ad_pseudobulk = ch_h5ad_pseudobulk // channel: [ integration, h5ad ]
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: subworkflows/local/singler/main.nf:43:5: Emit name should be omitted when there is only one emit

        obs      = ch_obs
    ^^^^^^^^^^

  • Warning: subworkflows/local/unify_genes/main.nf:36:5: Emit name should be omitted when there is only one emit

        h5ad = ch_h5ad // channel: [ meta, h5ad ]
    ^^^^^^^^^^^^

  • Warning: subworkflows/nf-core/h5ad_removebackground_barcodes_cellbender_anndata/main.nf:18:5: Emit name should be omitted when there is only one emit

        h5ad = ANNDATA_BARCODES.out.h5ad  // channel: [ val(meta), path(h5ad) ]
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:43:5: Emit name should be omitted when there is only one emit

        dummy_emit = true
    ^^^^^^^^^^^^^^^

  • Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5: Emit name should be omitted when there is only one emit

        valid_config = valid_config
    ^^^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5: Emit name should be omitted when there is only one emit

        dummy_emit = true
    ^^^^^^^^^^^^^^^