Skip to content

stableexpression_lint.md

Latest commit

 

History

History
245 lines (175 loc) · 8.86 KB

stableexpression_lint.md

File metadata and controls

245 lines (175 loc) · 8.86 KB

Nextflow lint results

  • Generated: 2026-03-18T00:27:14.834241617Z
  • Nextflow version: 26.02.0-edge
  • Summary: 34 warnings

⚠️ Warnings

  • Warning: modules/local/compute_dataset_statistics/main.nf:21:9: Variable was declared but not used

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

  • Warning: modules/local/expressionatlas/getaccessions/main.nf:31:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def keywords_string = keywords.split(',').collect { it.trim() }.join(' ')
                                                        ^^

  • Warning: modules/local/geo/getaccessions/main.nf:33:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def keywords_string = keywords.split(',').collect { it.trim() }.join(' ')
                                                        ^^

  • Warning: subworkflows/local/download_public_datasets/main.nf:24:5: Variable was declared but not used

        ch_fetched_accessions = channel.empty()
    ^^^^^^^^^^^^^^^^^^^^^

  • Warning: subworkflows/local/expression_normalisation/main.nf:31:15: Parameter was not used -- prefix with _ to suppress warning

            meta, file ->
              ^^^^

  • Warning: subworkflows/local/expression_normalisation/main.nf:36:74: Parameter was not used -- prefix with _ to suppress warning

        ch_raw_rnaseq_datasets_to_normalise = ch_datasets.raw.filter { meta, file -> meta.platform == 'rnaseq' }
                                                                         ^^^^

  • Warning: subworkflows/local/genorm/main.nf:96:17: Parameter was not used -- prefix with _ to suppress warning

                    meta, i, file_i, j, file_j -> i <= j } // keeps only pairs where i <= j
                ^^^^

  • Warning: subworkflows/local/genorm/main.nf:96:26: Parameter was not used -- prefix with _ to suppress warning

                    meta, i, file_i, j, file_j -> i <= j } // keeps only pairs where i <= j
                         ^^^^^^

  • Warning: subworkflows/local/genorm/main.nf:96:37: Parameter was not used -- prefix with _ to suppress warning

                    meta, i, file_i, j, file_j -> i <= j } // keeps only pairs where i <= j
                                    ^^^^^^

  • Warning: subworkflows/local/get_public_accessions/main.nf:77:35: Parameter was not used -- prefix with _ to suppress warning

                            .filter { species_name, quota -> quota == "ok" }
                                  ^^^^^^^^^^^^

  • Warning: subworkflows/local/get_public_accessions/main.nf:78:46: Parameter was not used -- prefix with _ to suppress warning

                            .map { species_name, quota -> species_name }
                                             ^^^^^

  • Warning: subworkflows/local/get_public_accessions/main.nf:114:55: Parameter was not used -- prefix with _ to suppress warning

                                        .map { accession, excluded_accessions -> accession }
                                                      ^^^^^^^^^^^^^^^^^^^

  • Warning: subworkflows/local/idmapping/main.nf:63:40: Implicit closure parameter is deprecated, declare an explicit parameter instead

                                    .map { it.trim() }
                                       ^^

  • Warning: subworkflows/local/merge_data/main.nf:25:71: Parameter was not used -- prefix with _ to suppress warning

        ch_normalised_rnaseq_counts = ch_normalised_counts.filter { meta, file -> meta.platform == "rnaseq" }
                                                                      ^^^^

  • Warning: subworkflows/local/merge_data/main.nf:26:75: Parameter was not used -- prefix with _ to suppress warning

        ch_normalised_microarray_counts = ch_normalised_counts.filter { meta, file -> meta.platform == "microarray" }
                                                                          ^^^^

  • Warning: subworkflows/local/merge_data/main.nf:29:44: Parameter was not used -- prefix with _ to suppress warning

                                        .map { meta, file -> file }
                                           ^^^^

  • Warning: subworkflows/local/merge_data/main.nf:34:48: Parameter was not used -- prefix with _ to suppress warning

                                            .map { meta, file -> file }
                                               ^^^^

  • Warning: subworkflows/local/merge_data/main.nf:49:44: Parameter was not used -- prefix with _ to suppress warning

                                        .map { meta, file -> file }
                                           ^^^^

  • Warning: subworkflows/local/merge_data/main.nf:71:35: Parameter was not used -- prefix with _ to suppress warning

                                meta, file -> // extracts design file and adds batch column whenever missing (for custom datasets)
                                  ^^^^

  • Warning: subworkflows/local/reporting/main.nf:46:32: Implicit closure parameter is deprecated, declare an explicit parameter instead

                            .map { it.trim() }
                               ^^

  • Warning: subworkflows/local/reporting/main.nf:47:35: Implicit closure parameter is deprecated, declare an explicit parameter instead

                            .filter { it != "" }
                                  ^^

  • Warning: subworkflows/local/reporting/main.nf:57:28: Parameter was not used -- prefix with _ to suppress warning

            ch_all_counts.map{ meta, file -> file }.collect(),
                           ^^^^

  • Warning: subworkflows/local/reporting/main.nf:76:28: Parameter was not used -- prefix with _ to suppress warning

            ch_all_counts.map{ meta, file -> file }.collect(),
                           ^^^^

  • Warning: subworkflows/local/utils_nfcore_stableexpression_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_stableexpression_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_stableexpression_pipeline/main.nf:235:19: Parameter was not used -- prefix with _ to suppress warning

                meta, file ->
                  ^^^^

  • Warning: subworkflows/local/utils_nfcore_stableexpression_pipeline/main.nf:252:16: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, file ->
               ^^^^

  • Warning: subworkflows/local/utils_nfcore_stableexpression_pipeline/main.nf:354:13: Implicit closure parameter is deprecated, declare an explicit parameter instead

                it.get(1).size() == 2 // only groups with two files
            ^^

  • Warning: subworkflows/local/utils_nfcore_stableexpression_pipeline/main.nf:357:13: Parameter was not used -- prefix with _ to suppress warning

                meta, files ->
            ^^^^

  • 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/stableexpression.nf:44:5: Variable was declared but not used

        ch_most_stable_genes_summary           = channel.empty()
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: workflows/stableexpression.nf:45:5: Variable was declared but not used

        ch_all_genes_statistics                = channel.empty()
    ^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: workflows/stableexpression.nf:46:5: Variable was declared but not used

        ch_most_stable_genes_transposed_counts = channel.empty()
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

  • Warning: workflows/stableexpression.nf:187:40: Parameter was not used -- prefix with _ to suppress warning

                ch_all_imputed_counts.map{ meta, file -> file },
                                       ^^^^