Mercurial > repos > mingchen0919 > aurora_star
comparison rmarkdown_report.Rmd @ 0:25602263cff0 draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author | mingchen0919 |
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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 |