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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 14:04:22 -0500
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---
title: 'Mapping evaluation'
output:
    html_document:
      highlight: pygments
---

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


```{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```')
```