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1 ---
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2 title: 'Skewer Trimming'
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3 output: html_document
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4 ---
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5
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6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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7 knitr::opts_chunk$set(
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8 echo = as.logical(opt$X_e),
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9 error = TRUE
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10 )
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11 ```
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12
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13
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14 # Run Skewer
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15
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16 ```{bash}
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17 cd ${X_d}
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18
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19 cat >temp.sh <<EOL
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20 skewer \\
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21 -q ${X_A} \\
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22 -Q ${X_B} \\
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23 -x ${X_x} \\
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24 -y ${X_y} \\
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25 ${X_X} \\
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26 ${X_Y} \\
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27 -o ${X_d}/trim > /dev/null 2>&1
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28 EOL
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29
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30 grep -v None temp.sh > skewer-job.sh
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31
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32 # run skewer
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33 sh skewer-job.sh
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34
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35 cp trim-trimmed-pair1.fastq ${X_f}
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36 cp trim-trimmed-pair2.fastq ${X_r}
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37 mv trim-trimmed.log trim-trimmed.txt
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38 ```
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39
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40
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41 ```{r}
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42 # display skewer job script
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43 skewer_sh = paste0(opt$X_d, '/skewer-job.sh')
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44 tags$code(tags$pre(readChar(skewer_sh, file.info(skewer_sh)$size )))
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45 ```
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46
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47 # Results
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48
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49 ```{r}
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50 tags$ul(
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51 tags$li(tags$a(href = 'trim-trimmed.txt', 'trim-trimmed.log')),
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52 tags$li(tags$a(href = 'trim-trimmed-pair1.fastq', 'trim-trimmed-pair1.fastq')),
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53 tags$li(tags$a(href = 'trim-trimmed-pair2.fastq', 'trim-trimmed-pair2.fastq'))
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54 )
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55 ```
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56
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