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2
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1 ---
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14
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2 title: 'HTML report title'
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3 output:
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4 html_document:
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5 number_sections: true
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6 toc: true
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7 theme: cosmo
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8 highlight: tango
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2
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9 ---
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10
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14
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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12 knitr::opts_chunk$set(
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13 echo = ECHO
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14 )
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2
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15 ```
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16
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17
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14
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18 # Fastqc Analysis
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2
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19
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14
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20 * Copy fastq files to job working directory
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21
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22 ```{bash 'copy files'}
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2
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23 for f in $(echo READS | sed "s/,/ /g")
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24 do
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25 cp $f ./
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26 done
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27 ```
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28
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14
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29 * Run fastqc
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2
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30
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14
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31 ```{bash 'run fastqc'}
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2
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32 for r in $(ls *.dat)
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33 do
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14
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34 fastqc -o REPORT_DIR $r > /dev/null 2>&1
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2
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35 done
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36 ```
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37
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14
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38 * Create links to original HTML reports
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2
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39
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|
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40 ```{r 'html report links'}
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41 html_report_list = list()
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14
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42 html_files = list.files('REPORT_DIR', pattern = '.*html')
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2
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43 for (i in html_files) {
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44 html_report_list[[i]] = tags$li(tags$a(href=i, i))
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45 }
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46 tags$ul(html_report_list)
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47 ```
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48
|
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14
|
49 # Fastqc output summary
|
|
2
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50
|
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14
|
51 * Define a function to extract outputs for each module from fastqc output
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|
2
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52
|
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14
|
53 ```{r 'function definition'}
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|
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54 extract_data_module = function(fastqc_data, module_name) {
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|
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55 f = readLines(fastqc_data)
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|
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56 start_line = grep(module_name, f)
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|
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57 end_module_lines = grep('END_MODULE', f)
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|
|
58 end_line = end_module_lines[which(end_module_lines > start_line)[1]]
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|
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59 module_data = f[(start_line+1):(end_line-1)]
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|
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60 writeLines(module_data, 'temp.txt')
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|
|
61 read.csv('temp.txt', sep = '\t')
|
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2
|
62 }
|
|
|
63 ```
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|
|
64
|
|
14
|
65 ##
|
|
2
|
66
|
|
14
|
67 # Session Info
|
|
2
|
68
|
|
14
|
69 ```{r 'session info'}
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|
|
70 sessionInfo()
|
|
2
|
71 ```
|
|
|
72
|
