diff --git a/CHANGELOG.md b/CHANGELOG.md index 86fa2680..bb031ee5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -61,6 +61,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- [[#646](https://github.com/nf-core/differentialabundance/pull/646)] - Remove the `--differential_feature_name_column` parameter and consolidate its functionality into `--features_name_col` ([@delfiterradas](https://github.com/delfiterradas), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)). - [[#652](https://github.com/nf-core/differentialabundance/pull/652)] - Harmonize `--contrasts` and `--contrasts_yml` ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)). - [[#626](https://github.com/nf-core/differentialabundance/pull/626)] - Update documentation, bump Nextflow version, `versions.yml` output cleanup and add params_yaml to report bundle ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila), [@apeltzer](https://github.com/apeltzer), [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)). - [[#628](https://github.com/nf-core/differentialabundance/pull/628)] - Removed `--deseq2_cores` parameter and infer from task cpus instead,([@delfiterradas](https://github.com/delfiterradas), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)). diff --git a/assets/differentialabundance_report.qmd b/assets/differentialabundance_report.qmd index 25ed0b45..13188b77 100644 --- a/assets/differentialabundance_report.qmd +++ b/assets/differentialabundance_report.qmd @@ -1174,9 +1174,9 @@ foo <- lapply(names(p_value_types), function(pvt) { # Determine which column to use for labels if (!is.null(params$meta$params$features) && - !is.null(params$meta$params$differential_feature_name_column) && - (params$meta$params$differential_feature_name_column %in% colnames(differential_results[[1]]))) { - label_col <- params$meta$params$differential_feature_name_column + !is.null(params$meta$params$features_name_col) && + (params$meta$params$features_name_col %in% colnames(differential_results[[1]]))) { + label_col <- params$meta$params$features_name_col } else { label_col <- params$meta$params$differential_feature_id_column } @@ -1258,9 +1258,9 @@ for (i in 1:nrow(contrasts)) { # Labels: prefer feature name if present if (!is.null(params$features) && - !is.null(params$meta$params$differential_feature_name_column) && - (params$meta$params$differential_feature_name_column %in% colnames(full_de))) { - label_col <- params$meta$params$differential_feature_name_column + !is.null(params$meta$params$features_name_col) && + (params$meta$params$features_name_col %in% colnames(full_de))) { + label_col <- params$meta$params$features_name_col } else { label_col <- params$meta$params$differential_feature_id_column } diff --git a/conf/paramsheet.yaml b/conf/paramsheet.yaml index ab1ace6b..356575e2 100644 --- a/conf/paramsheet.yaml +++ b/conf/paramsheet.yaml @@ -7,7 +7,6 @@ features_name_col: gene_name features_metadata_cols: gene_id,gene_name,gene_biotype differential_feature_id_column: gene_id - differential_feature_name_column: gene_name observations_id_col: sample observations_name_col: sample @@ -111,7 +110,6 @@ differential_pval_column: P.Value differential_qval_column: adj.P.Val differential_feature_id_column: PROBEID - differential_feature_name_column: SYMBOL shinyngs_build_app: true @@ -145,7 +143,6 @@ differential_pval_column: P.Value differential_qval_column: adj.P.Val differential_feature_id_column: ID - differential_feature_name_column: Symbol - paramset_name: limma_maxquant differential_method: limma @@ -167,7 +164,6 @@ differential_pval_column: P.Value differential_qval_column: adj.P.Val differential_feature_id_column: Majority protein IDs - differential_feature_name_column: Majority protein IDs proteus_measurecol_prefix: LFQ intensity diff --git a/nextflow.config b/nextflow.config index 203f3802..7457e35f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -90,7 +90,6 @@ params { differential_method = 'deseq2' // 'deseq2', 'limma', 'dream' differential_file_suffix = null differential_feature_id_column = "gene_id" - differential_feature_name_column = "gene_name" differential_fc_column = "log2FoldChange" differential_pval_column = "pvalue" differential_qval_column = "padj" diff --git a/nextflow_schema.json b/nextflow_schema.json index 58709a31..77122ea5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -557,12 +557,6 @@ "description": "Maximum q value used to calculate differential feature numbers", "fa_icon": "fas fa-angle-double-up" }, - "differential_feature_name_column": { - "type": "string", - "default": "gene_name", - "description": "Where a features file (GTF) has been provided, what attribute to use to name features", - "fa_icon": "fas fa-signature" - }, "differential_foldchanges_logged": { "type": "boolean", "default": true,