Adding a differential expression process

main.nf

@@ -276,3 +276,22 @@ process multiqc {
     --cl_config "extra_fn_clean_exts: [ '_1', '_2' ]"
   """
 }
+
+process differential_expression {
+
+  publishDir "reports"
+
+  input:
+  file annotation from annotation_for_de
+  file salmon from salmon_for_de.collect()
+  file sample_info from sample_info_for_de
+
+  output:
+  file "*.html"
+
+  script:
+  """
+  cp ${baseDir}/bin/*.R* .
+  Rscript -e 'rmarkdown::render("differential_expression.Rmd", params = list(annotation_file = "${annotation}"))'
+  """
+}