---
title: 'Index genome'
output:
    html_document:
      highlight: pygments
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(error = TRUE, echo = FALSE)
```

## Job scripts

```{bash, echo=FALSE}
sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh
```

### Index genome

```{r echo=FALSE,results='asis'}
# display content of the job-script.sh file.
cat('```bash\n')
cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/index-genome.sh')), sep = '\n')
cat('\n```')
```