diff skewer.Rmd @ 1:e969699f49b6 draft

working version

--- a/skewer.Rmd	Thu Mar 01 14:25:15 2018 -0500
+++ b/skewer.Rmd	Fri Mar 02 09:59:25 2018 -0500
@@ -1,29 +1,56 @@
 ---
-title: 'HTML report title'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
+title: 'Skewer Trimming'
+output: html_document
 ---
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
 knitr::opts_chunk$set(
-  echo = as.logical(), 
+  echo = as.logical(opt$X_e), 
   error = TRUE
 )
 ```
 
 
-# Code for computational analysis
+# Run Skewer
 
-```{r 'step 1'}
+```{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
 
-```{r 'ste[ 2'}
+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'))
+)
+```
+