fix gprofiler links

Author: SusiJo

assets/differentialabundance_report.Rmd

@@ -1025,10 +1025,11 @@ if (!is.null(params$functional_method)){
         ifelse(params$gprofiler2_significant, paste0(" Enrichment was only considered if significant, i.e. adjusted p-value <= ", params$gprofiler2_max_qval, "."), "Enrichment was also considered if not significant."), "\n"))
 
         # Make sure to grab only non-empty files
-        for (name in differential_names) {
+        for (i in seq_along(differential_names)) {
+            name <- differential_names[i]
             cat(paste0("\n##### ", name, "\n"))
 
-            table <- paste0(name, ".gprofiler2.all_enriched_pathways.tsv")
+            table <- paste0(contrasts$id[i], ".gprofiler2.all_enriched_pathways.tsv")
             table_path <- file.path(params$input_dir, table)
             if (!file.exists(table_path) || file.size(table_path) == 0){
                 cat(paste0("No ", ifelse(params$gprofiler2_significant, "significantly", ""), " enriched pathways were found for this contrast."))