---
title: 'Build collection: a paired datasets'
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
)
```

# Command line arguments

```{r 'command line arguments'}
str(opt)
```

# Rename files

```{r}
dir.create('files_directory')
file.copy("FORWARD_INPUT", './files_directory/forward.FORMAT')
file.copy("REVERSE_INPUT", './files_directory/reverse.FORMAT')
```

