diff 04_mapping_evaluation.Rmd @ 3:42f9bad52d54 draft

planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/04_mapping_evaluation.Rmd	Tue May 01 10:42:30 2018 -0400
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+---
+title: 'Mapping evaluation'
+output:
+    html_document:
+      highlight: pygments
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(error = TRUE, echo = FALSE)
+```
+
+### Mapping evaluation
+
+```{r echo=FALSE,warning=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.sh')), sep = '\n')
+cat('\n```')
+```
+
+
+### Mapping evaluation results
+
+```{r echo=FALSE,warning=FALSE,results='asis'}
+# display content of the job-script.sh file.
+cat('```bash\n')
+cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/flagstat.txt')), sep = '\n')
+cat('\n```')
+```