---
title: 'Collection builder (collection type: list)'
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}
str(opt)
```


```{bash 'copy data to working directory'}
mkdir files_directory
# Copy uploaded data to the working directory
for f in $(echo FILE_LIST | sed "s/,/ /g")
do
    cp $f ./files_directory/$f.fastqsanger
done
```
