diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk index 6efe71ca..51d3754d 100644 --- a/workflow/rules/datavzrd.smk +++ b/workflow/rules/datavzrd.smk @@ -67,7 +67,7 @@ rule spia_datavzrd: log: "logs/datavzrd-report/spia-{model}/spia-{model}.log", wrapper: - "v1.29.0/utils/datavzrd" + "v2.6.0/utils/datavzrd" rule diffexp_datavzrd: @@ -92,7 +92,7 @@ rule diffexp_datavzrd: log: "logs/datavzrd-report/diffexp.{model}/diffexp.{model}.log", wrapper: - "v1.29.0/utils/datavzrd" + "v2.6.0/utils/datavzrd" rule go_enrichment_datavzrd: @@ -119,4 +119,4 @@ rule go_enrichment_datavzrd: log: "logs/datavzrd-report/go_enrichment-{model}/go_enrichment-{model}_{gene_fdr}.go_term_fdr_{go_term_fdr}.log", wrapper: - "v1.29.0/utils/datavzrd" + "v2.6.0/utils/datavzrd" diff --git a/workflow/rules/trim_3prime.smk b/workflow/rules/trim_3prime.smk index 624cc8cf..a038bfdf 100644 --- a/workflow/rules/trim_3prime.smk +++ b/workflow/rules/trim_3prime.smk @@ -1,5 +1,4 @@ if is_3prime_experiment and three_prime_vendor == "lexogen": - # Rule cutadapt1 checks and removes poly-A tails and sequence qualilty score <20. # reasoning behind parameters: # * `-m 20`: diff --git a/workflow/scripts/plot_diffexp_heatmap.R b/workflow/scripts/plot_diffexp_heatmap.R index c31ace8d..4180992b 100644 --- a/workflow/scripts/plot_diffexp_heatmap.R +++ b/workflow/scripts/plot_diffexp_heatmap.R @@ -53,7 +53,7 @@ if (all(selectedgenes == 0)) { # If number of transcripts is more than 100, # Since for RNA-seq multiple transcripts may present for a single gene. } else if (nrow(selectedgenes) > 100) { - pdf_height <- round(nrow(selectedgenes) / 7) + pdf_height <- round(nrow(selectedgenes) / 5) pdf(snakemake@output[["diffexp_heatmap"]], height = pdf_height, width = ncol(selectedgenes) * 2 ) @@ -63,7 +63,7 @@ if (all(selectedgenes == 0)) { ) dev.off() } else { - pdf_height <- round(nrow(selectedgenes) / 7) + pdf_height <- round(nrow(selectedgenes) / 5) pdf( file = snakemake@output[["diffexp_heatmap"]], height = pdf_height, width = ncol(selectedgenes) * 2 diff --git a/workflow/scripts/spia.R b/workflow/scripts/spia.R index fa68a664..dbd41a5f 100644 --- a/workflow/scripts/spia.R +++ b/workflow/scripts/spia.R @@ -21,7 +21,6 @@ diffexp <- read_tsv(snakemake@input[["diffexp"]]) %>% mutate(ens_gene = str_c("ENSEMBL:", ens_gene)) universe <- diffexp %>% pull(var = ens_gene) sig_genes <- diffexp %>% filter(qval <= 0.05) - if (nrow(sig_genes) == 0) { cols <- c( "Name", "Status", "Combined FDR", @@ -30,7 +29,7 @@ if (nrow(sig_genes) == 0) { "Combined Bonferroni p-values", "p-value to observe a total accumulation", "Combined p-value", "Ids" ) - res <- data.frame(matrix(ncol = 7, nrow = 0, dimnames = list(NULL, cols))) + res <- data.frame(matrix(ncol = 11, nrow = 0, dimnames = list(NULL, cols))) # create empty perturbation plots pdf(file = snakemake@output[["plots"]]) write_tsv(res, snakemake@output[["table"]])