diff --git a/drop/template/Scripts/Pipeline/SampleAnnotation.R b/drop/template/Scripts/Pipeline/SampleAnnotation.R index eea616ac..6296a413 100644 --- a/drop/template/Scripts/Pipeline/SampleAnnotation.R +++ b/drop/template/Scripts/Pipeline/SampleAnnotation.R @@ -26,6 +26,7 @@ suppressPackageStartupMessages({ }) sa <- fread(snakemake@input$sampleAnnotation) +hpo_file <- snakemake@params$hpo_file #' #' Number of rows and columns in the sample annotation: `r dim(sa)` @@ -80,7 +81,7 @@ unique(sa[,.(RNA_ID, DROP_GROUP)])$DROP_GROUP %>% strsplit(',') %>% unlist %>% if(!is.null(sa$HPO_TERMS) & !all(is.na(sa$HPO_TERMS)) & ! all(sa$HPO_TERMS == '')){ sa2 <- sa[, .SD[1], by = RNA_ID] - filename <- ifelse(is.null(snakemake@params$hpo_file), + filename <- ifelse(is.null(hpo_file), 'https://www.cmm.in.tum.de/public/paper/drop_analysis/resource/hpo_genes.tsv.gz', hpo_file) hpo_dt <- fread(filename)