--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/01_skewer_analysis.Rmd	Sun Dec 30 12:55:49 2018 -0500
@@ -0,0 +1,65 @@
+---
+title: 'Skewer Analysis'
+output:
+    html_document:
+      highlight: pygments
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(error = TRUE, echo = FALSE)
+```
+
+
+## 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)
+```
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