view skewer.Rmd @ 1:e969699f49b6 draft

working version

---
title: 'Skewer Trimming'
output: html_document
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = as.logical(opt$X_e), 
  error = TRUE
)
```


# Run Skewer

```{bash}
cd ${X_d}

cat >temp.sh <<EOL
skewer \\
  -q ${X_A} \\
  -Q ${X_B} \\
  -x ${X_x} \\
  -y ${X_y} \\
  ${X_X} \\
  ${X_Y} \\
  -o ${X_d}/trim > /dev/null 2>&1
EOL

grep -v None temp.sh > skewer-job.sh

# run skewer
sh skewer-job.sh

cp trim-trimmed-pair1.fastq ${X_f}
cp trim-trimmed-pair2.fastq ${X_r}
mv trim-trimmed.log trim-trimmed.txt
```


```{r}
# display skewer job script
skewer_sh = paste0(opt$X_d, '/skewer-job.sh')
tags$code(tags$pre(readChar(skewer_sh, file.info(skewer_sh)$size )))
```

# Results

```{r}
tags$ul(
  tags$li(tags$a(href = 'trim-trimmed.txt', 'trim-trimmed.log')),
  tags$li(tags$a(href = 'trim-trimmed-pair1.fastq', 'trim-trimmed-pair1.fastq')),
  tags$li(tags$a(href = 'trim-trimmed-pair2.fastq', 'trim-trimmed-pair2.fastq'))
)
```