---
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')
```



