diff rmarkdown_samtools_flagstat.Rmd @ 1:a0f0effea707 draft

fix wrong input type error

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_samtools_flagstat.Rmd	Wed Dec 27 11:55:46 2017 -0500
@@ -0,0 +1,28 @@
+---
+title: 'HTML report title'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO,
+  error = TRUE
+)
+```
+
+
+# Code for computational analysis
+
+```{r 'step 1'}
+command = paste0('samtools flagstat ', opt$input_bam, ' > report.csv')
+system(command)
+read.csv('report.csv')
+```
+
+
+