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"--fc_threshold", + "--logFC_threshold", type = "double", default = 1.1, metavar = "number", @@ -139,7 +139,7 @@ required$add_argument( ) required$add_argument( - "--pval_cutoff", + "--padj_cutoff", type = "double", default = 0.05, metavar = "number", @@ -254,8 +254,6 @@ de_results <- perform_de( ref_class = args$ref_class, confounding_vars = args$confounding_vars, random_effects_var = args$random_effects_var, - fc_threshold = args$fc_threshold, - pval_cutoff = args$pval_cutoff, mast_method = args$mast_method, force_run = args$force_run, ensembl_mapping_file = args$ensembl_mappings, @@ -278,8 +276,8 @@ for (result in names(de_results)) { ) report_de(de_results[[result]], - fc_threshold = args$fc_threshold, - pval_cutoff = args$pval_cutoff, + logFC_threshold = args$logFC_threshold, + padj_cutoff = args$padj_cutoff, n_label = args$n_label, report_folder_path = file.path(getwd()), report_file = paste0(file_name, result, "_scflow_de_report") @@ -289,8 +287,8 @@ for (result in names(de_results)) { p <- scFlow::volcano_plot( dt = de_results[[result]], - fc_threshold = args$fc_threshold, - pval_cutoff = args$pval_cutoff, + logFC_threshold = args$logFC_threshold, + padj_cutoff = args$padj_cutoff, n_label = args$n_label ) diff --git a/bin/scflow_ipa.r b/bin/scflow_ipa.r index 5e09573..39b816c 100755 --- a/bin/scflow_ipa.r +++ b/bin/scflow_ipa.r @@ -64,7 +64,7 @@ required$add_argument( ) required$add_argument( - "--fc_threshold", + "--logFC_threshold", type = "double", default = 1.1, metavar = "number", @@ -72,7 +72,7 @@ required$add_argument( ) required$add_argument( - "--pval_cutoff", + "--padj_cutoff", type = "double", default = 0.05, metavar = "number", @@ -121,8 +121,8 @@ for (gene_file in args$gene_file) { dt <- dt %>% dplyr::filter( - padj <= args$pval_cutoff, - abs(logFC) >= log2(args$fc_threshold) + padj <= args$padj_cutoff, + abs(logFC) >= log2(args$logFC_threshold) ) if (nrow(dt) < 5) { diff --git a/bin/scflow_map_celltypes.r b/bin/scflow_map_celltypes.r index 5c913dd..7ec9204 100755 --- a/bin/scflow_map_celltypes.r +++ b/bin/scflow_map_celltypes.r @@ -53,6 +53,15 @@ required$add_argument( required = TRUE ) +required$add_argument( + "--annotation_level", + default = 1, + type = "integer", + help = "the annotation level of the reference ctd", + required = TRUE, + metavar = "N" +) + required$add_argument( "--species", help = "the biological species (e.g. mouse, human)", @@ -101,6 +110,7 @@ sce <- map_celltypes_sce( ctd_folder = args$ctd_folder, clusters_colname = args$clusters_colname, cells_to_sample = args$cells_to_sample, + annotation_level = as.numeric(args$annotation_level), species = args$species ) diff --git a/bin/scflow_reduce_dims.r b/bin/scflow_reduce_dims.r index 3ed29ae..2788e95 100755 --- a/bin/scflow_reduce_dims.r +++ b/bin/scflow_reduce_dims.r @@ -313,6 +313,7 @@ args <- purrr::map(args, function(x) { sce <- read_sce(args$sce_path, read_metadata = TRUE) +set.seed(42) sce <- reduce_dims_sce( sce, input_reduced_dim = args$input_reduced_dim, diff --git a/conf/base.config b/conf/base.config old mode 100644 new mode 100755 diff --git a/conf/gcp.config b/conf/gcp.config old mode 100644 new mode 100755 diff --git a/conf/igenomes.config b/conf/igenomes.config old mode 100644 new mode 100755 diff --git a/conf/modules.config b/conf/modules.config old mode 100644 new mode 100755 diff --git a/conf/scflow_analysis.config b/conf/scflow_analysis.config old mode 100644 new mode 100755 index 79493ec..591e8f8 --- a/conf/scflow_analysis.config +++ b/conf/scflow_analysis.config @@ -115,6 +115,7 @@ params { // Options: Celltype Annotation cta_clusters_colname = 'clusters' cta_cells_to_sample = 10000 + cta_annotation_level = 2 // Options: Celltype Metrics Report cta_unique_id_var = 'manifest' @@ -137,8 +138,8 @@ params { dge_ref_class = 'Control' dge_confounding_vars = 'cngeneson' // * dge_random_effects_var = 'null' - dge_fc_threshold = 1.1 - dge_pval_cutoff = 0.05 + dge_logFC_threshold = 0.25 + dge_padj_cutoff = 0.05 dge_n_label = 5 dge_force_run = 'false' dge_max_cores = 'null' diff --git a/conf/test.config b/conf/test.config old mode 100644 new mode 100755 diff --git a/conf/test_full.config b/conf/test_full.config old mode 100644 new mode 100755 diff --git a/docs/README.md b/docs/README.md old mode 100644 new mode 100755 diff --git a/docs/images/nf-core-scflow_logo.png b/docs/images/nf-core-scflow_logo.png old mode 100644 new mode 100755 diff --git a/docs/images/scflow_workflow.png b/docs/images/scflow_workflow.png old mode 100644 new mode 100755 diff --git a/docs/output.md b/docs/output.md old mode 100644 new mode 100755 diff --git a/docs/usage.md b/docs/usage.md old mode 100644 new mode 100755 diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar old mode 100644 new mode 100755 diff --git a/main.nf b/main.nf old mode 100644 new mode 100755 diff --git a/modules.json b/modules.json old mode 100644 new mode 100755 diff --git a/modules/local/functions.nf b/modules/local/functions.nf old mode 100644 new mode 100755 diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/functions.nf b/modules/local/process/functions.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/checkinputs.nf b/modules/local/process/scflow/checkinputs.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/cluster.nf b/modules/local/process/scflow/cluster.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/dge.nf b/modules/local/process/scflow/dge.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/dirichlet.nf b/modules/local/process/scflow/dirichlet.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/finalize.nf b/modules/local/process/scflow/finalize.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/functions.nf b/modules/local/process/scflow/functions.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/integrate.nf b/modules/local/process/scflow/integrate.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/ipa.nf b/modules/local/process/scflow/ipa.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/mapcelltypes.nf b/modules/local/process/scflow/mapcelltypes.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/merge.nf b/modules/local/process/scflow/merge.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/mergeqctables.nf b/modules/local/process/scflow/mergeqctables.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/plotreddimgenes.nf b/modules/local/process/scflow/plotreddimgenes.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/qc.nf b/modules/local/process/scflow/qc.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/reducedims.nf b/modules/local/process/scflow/reducedims.nf old mode 100644 new mode 100755 diff --git a/modules/local/process/scflow/reportintegrated.nf b/modules/local/process/scflow/reportintegrated.nf old mode 100644 new mode 100755 diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf old mode 100644 new mode 100755 diff --git a/nextflow.config b/nextflow.config old mode 100644 new mode 100755 diff --git a/nextflow_schema.json b/nextflow_schema.json old mode 100644 new mode 100755 index 8771107..c9a0516 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -826,6 +826,11 @@ "default": 10000, "description": "Max cells to sample." }, + "cta_annotation_level": { + "type": "integer", + "default": 1, + "description": "Annotation level of the reference ctd" + }, "cta_unique_id_var": { "type": "string", "default": "individual", @@ -856,6 +861,7 @@ "required": [ "cta_clusters_colname", "cta_cells_to_sample", + "cta_annotation_level", "cta_unique_id_var", "cta_celltype_var", "cta_facet_vars", @@ -947,13 +953,13 @@ "description": "Random effect confounding variable.", "help_text": "If specified, the term `+ (1 | x ) +`is added to the model, where x is the specified random effects variable." }, - "dge_fc_threshold": { + "dge_logFC_threshold": { "type": "number", "default": 1.1, "description": "Fold-change threshold for plotting.", "help_text": "This absolute fold-change cut-off value is used in plots (e.g. volcano) and the DGE report." }, - "dge_pval_cutoff": { + "dge_padj_cutoff": { "type": "number", "default": 0.05, "description": "Adjusted p-value cutoff.", @@ -993,8 +999,8 @@ "dge_ref_class", "dge_confounding_vars", "dge_random_effects_var", - "dge_fc_threshold", - "dge_pval_cutoff", + "dge_logFC_threshold", + "dge_padj_cutoff", "dge_n_label", "dge_force_run", "dge_max_cores" diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf old mode 100644 new mode 100755 diff --git a/workflows/scflow.nf b/workflows/scflow.nf old mode 100644 new mode 100755 index d79ff84..d62b227 --- a/workflows/scflow.nf +++ b/workflows/scflow.nf @@ -167,6 +167,7 @@ def scflow_mapcelltypes_options = modules['scflow_mapcelltypes'] scflow_mapcelltypes_options.args = "--clusters_colname ${params.cta_clusters_colname} \ --cells_to_sample ${params.cta_cells_to_sample} \ + --annotation_level ${params.cta_annotation_level} \ --species ${params.species} \ --reddimplot_pointsize ${params.reddimplot_pointsize} \ --reddimplot_alpha ${params.reddimplot_alpha}" @@ -198,8 +199,8 @@ scflow_dge_options.args = --ref_class ${params.dge_ref_class} \ --confounding_vars ${params.dge_confounding_vars} \ --random_effects_var ${params.dge_random_effects_var} \ - --pval_cutoff ${params.dge_pval_cutoff} \ - --fc_threshold ${params.dge_fc_threshold} \ + --padj_cutoff ${params.dge_padj_cutoff} \ + --logFC_threshold ${params.dge_logFC_threshold} \ --species ${params.species} \ --max_cores ${params.dge_max_cores}" @@ -214,8 +215,8 @@ scflow_ipa_options.args = "--enrichment_tool ${params.ipa_enrichment_tool} \ --enrichment_method ${params.ipa_enrichment_method} \ --enrichment_database ${params.ipa_enrichment_database} \ - --pval_cutoff ${params.dge_pval_cutoff} \ - --fc_threshold ${params.dge_fc_threshold} \ + --padj_cutoff ${params.dge_padj_cutoff} \ + --logFC_threshold ${params.dge_logFC_threshold} \ --species ${params.species}" def scflow_dirichlet_options = modules['scflow_dirichlet']