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3
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1 ---
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2 title: 'Expose data (paired)'
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3 output: html_document
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4 ---
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5
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6 <style>
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7 pre code, pre, code {
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8 white-space: pre !important;
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9 overflow-x: scroll !important;
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10 word-break: keep-all !important;
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11 word-wrap: initial !important;
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12 }
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13 </style>
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14
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15 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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16 knitr::opts_chunk$set(error = TRUE)
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17 ```
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18
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19 ## User input
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20
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21 ```{r, echo=FALSE, eval=TRUE}
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22 ##-------- build script files -----------
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23
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24 # build script file: script.sh
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25 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
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26 sep = '|', header = TRUE)
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27
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28
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29 knitr::kable(df)
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30 ```
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31
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32 ```{r, echo=FALSE}
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33 # write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
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34 if (nrow(df) > 0) {
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35 for (i in 1:nrow(df)) {
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36 tool_output_dir = readLines(df[i, 'tool_output_dir'])[1]
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37 full_path = paste0(tool_output_dir, '/', df[i, 'relative_path'])
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38 if (dir.exists(full_path)) {
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39 from_files = list.files(full_path, full.names = TRUE)
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40 to_files = paste0(Sys.getenv('individual_outputs/'), list.files(full_path))
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41 file.copy(from = from_files, to = to_files)
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42 }
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43 if (file.exists(full_path)) {
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44 file.copy(from = full_path, to = paste0(Sys.getenv('individual_outputs/'), df[i, 'relative_path']))
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45 }
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46 # command_line = paste0('cp -r ', full_path, ' paired')
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47 # write(command_line, append = TRUE,
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48 # file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
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49 }
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50 }
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51 ```
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52
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53
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