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annotate 04_mapping_evaluation.Rmd @ 5:9681e90f3e28 draft

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planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
author mingchen0919
date Tue, 01 May 2018 11:15:25 -0400
parents 42f9bad52d54
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1 ---
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2 title: 'Mapping evaluation'
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3 output:
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4 html_document:
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5 highlight: pygments
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6 ---
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8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
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10 ```
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13 ```{r echo=FALSE,warning=FALSE,results='asis'}
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14 # display content of the job-script.sh file.
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15 cat('```bash\n')
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16 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.sh')), sep = '\n')
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17 cat('\n```')
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18 ```
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21 ### Mapping evaluation results
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23 ```{r echo=FALSE,warning=FALSE,results='asis'}
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24 # display content of the job-script.sh file.
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25 cat('```bash\n')
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26 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.txt')), sep = '\n')
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27 cat('\n```')
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28 ```