--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_report.Rmd	Fri Dec 14 00:40:15 2018 -0500
@@ -0,0 +1,111 @@
+---
+title: 'Aurora Skewer Report'
+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 script
+
+```{bash echo=FALSE}
+sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh
+```
+
+```{r echo=FALSE,warning=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/job-1-script.sh')), sep = '\n')
+cat('\n```')
+```
+
+# Results summary
+
+## Reads processing summary
+
+```{r echo=TRUE}
+log = readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/trim-trimmed.log'))
+start_line = grep('read.+processed; of these:', log)
+end_line = grep('untrimmed.+available after processing', log)
+processing_summary = gsub('(\\d+) ', '\\1\t', log[start_line:end_line])
+processing_summary_df = do.call(rbind, strsplit(processing_summary, '\t'))
+colnames(processing_summary_df) = c('Total reads:', processing_summary_df[1,1])
+knitr::kable(processing_summary_df[-1, ])
+```
+
+## Length distribution of reads after trimming
+
+```{r echo=TRUE, message=FALSE, warning=FALSE}
+start_line = grep('length	count	percentage', log)
+len_dist = log[(start_line):length(log)]
+len_dist = do.call(rbind, strsplit(len_dist, '\t'))
+columns = len_dist[1, ]
+len_dist = as.data.frame(len_dist[-1, ])
+colnames(len_dist) = columns
+
+library(plotly)
+library(ggplot2)
+len_dist$count = as.numeric(len_dist$count)
+labels = as.character(len_dist$length)
+len_dist$length = 1:nrow(len_dist)
+pp = ggplot(data = len_dist, aes(length, count)) +
+  geom_line(color='red') +
+  scale_x_continuous(name = 'Length',
+                   breaks = 1:nrow(len_dist),
+                   labels = labels) +
+  theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
+  ylab('Count') +
+  ggtitle('Length distribution')
+ggplotly(pp)
+```
+