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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 13:11:48 -0500
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1 ---
2 title: 'STAR: RNA-Seq aligner'
3 output:
4 html_document:
5 highlight: pygments
6 ---
7
8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
10 ```
11
12 ```{css, echo=FALSE}
13 pre code, pre, code {
14 white-space: pre !important;
15 overflow-x: scroll !important;
16 word-break: keep-all !important;
17 word-wrap: initial !important;
18 }
19 ```
20
21 ```{r, echo=FALSE}
22 # to make the css theme to work, <link></link> tags cannot be added directly
23 # as <script></script> tags as below.
24 # it has to be added using a code chunk with the htmltool functions!!!
25 css_link = tags$link()
26 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
27 css_link
28 ```
29
30 ```{r, eval=FALSE, echo=FALSE}
31 # this code chunk is purely for adding comments
32 # below is to add jQuery and jstree javascripts
33 ```
34
35 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
36
37
38 ```{r, eval=FALSE, echo=FALSE}
39 # this code chunk is purely for adding comments
40 # javascript code below is to build the file tree interface
41 # 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
42 ```
43 <script>
44 jQuery(function () {
45 // create an instance when the DOM is ready
46 jQuery('#jstree').jstree().bind("select_node.jstree", function (e, data) {
47 window.open( data.node.a_attr.href, data.node.a_attr.target )
48 });
49 });
50 </script>
51
52
53 ```{r, eval=FALSE, echo=FALSE}
54 ---
55 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
56 ---
57 ```
58
59 ## Job scripts
60
61 ```{bash, echo=FALSE}
62 sh ${TOOL_INSTALL_DIR}/build-and-run-job-scripts.sh
63 ```
64
65 ### Index genome
66
67 ```{r echo=FALSE,results='asis'}
68 # display content of the job-script.sh file.
69 cat('```bash\n')
70 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/index-genome.sh')), sep = '\n')
71 cat('\n```')
72 ```
73
74 ### Mapping
75
76 ```{r echo=FALSE,results='asis'}
77 # display content of the job-script.sh file.
78 cat('```bash\n')
79 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/mapping.sh')), sep = '\n')
80 cat('\n```')
81 ```
82
83 ### SAM to sorted BAM
84
85 ```{r echo=FALSE,warning=FALSE,results='asis'}
86 # display content of the job-script.sh file.
87 cat('```bash\n')
88 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/sam2bam.sh')), sep = '\n')
89 cat('\n```')
90 ```
91
92 ### Mapping evaluation
93
94 ```{r echo=FALSE,warning=FALSE,results='asis'}
95 # display content of the job-script.sh file.
96 cat('```bash\n')
97 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.sh')), sep = '\n')
98 cat('\n```')
99 ```
100
101
102 ### Mapping evaluation results
103
104 ```{r echo=FALSE,warning=FALSE,results='asis'}
105 # display content of the job-script.sh file.
106 cat('```bash\n')
107 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.txt')), sep = '\n')
108 cat('\n```')
109 ```
110