--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_flagstat.Rmd	Tue Dec 26 19:27:41 2017 -0500
@@ -0,0 +1,25 @@
+---
+title: 'samtools flagstat'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO
+)
+```
+
+
+# Code for computational analysis
+
+```{r 'run flagstat'}
+command = paste0('samtools flagstat ', opt$input_bam, ' > report.txt')
+system(command)
+```
+
+