---
title: 'STAR: RNA-Seq aligner'
output:
    html_document:
      highlight: pygments
---

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

```{css, echo=FALSE}
pre code, pre, code {
  white-space: pre !important;
  overflow-x: scroll !important;
  word-break: keep-all !important;
  word-wrap: initial !important;
}
```

```{r, echo=FALSE}
# to make the css theme to work, <link></link> tags cannot be added directly 
# as <script></script> tags as below.
# it has to be added using a code chunk with the htmltool functions!!!
css_link = tags$link()
css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
css_link
```

```{r, eval=FALSE, echo=FALSE}
# this code chunk is purely for adding comments
# below is to add jQuery and jstree javascripts
```

<script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>


```{r, eval=FALSE, echo=FALSE}
# this code chunk is purely for adding comments
# javascript code below is to build the file tree interface
# see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
```
<script>
  jQuery(function () {
    // create an instance when the DOM is ready
    jQuery('#jstree').jstree().bind("select_node.jstree", function (e, data) {
     window.open( data.node.a_attr.href, data.node.a_attr.target )
    });
  });
</script>


```{r, eval=FALSE, echo=FALSE}
---
# ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
---
```

## 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```')
```

### Mapping

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

### SAM to sorted BAM

```{r echo=FALSE,warning=FALSE,results='asis'}
# display content of the job-script.sh file.
cat('```bash\n')
cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/sam2bam.sh')), sep = '\n')
cat('\n```')
```

### Mapping evaluation

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


### Mapping evaluation results

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