diff split_fasta.Rmd @ 0:3918528c19b4 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split_fasta.Rmd	Mon Apr 09 11:51:32 2018 -0400
@@ -0,0 +1,45 @@
+---
+title: 'FASTA splitter'
+output: 
+  html_document:
+    highlight: pygments
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = TRUE, error = TRUE)
+```
+
+
+```{bash}
+# build job-script
+mkdir -p ${WORKING_DIR}/fasta_files
+
+# single-end.sh
+cat <<EOF >${X_d}/fasta_splitter.sh
+${WORKING_DIR}/fasta_files && \\
+  ${X_t}/split.pl ${X_A} ${X_B} > ${X_d}/fasta_splitter-log.txt 2>&1
+EOF
+```
+
+```{bash, 'run jobs', echo=FALSE}
+# run job script, always use absolute path. 
+# we want to run all jobs within the working path.
+sh ${X_d}/fasta_splitter.sh
+```
+
+```{r, 'display output directory contents', results='asis', echo=FALSE}
+## after the job is done, we list all files from the output directory.
+## full relative path to the output directory needs to be displayed.
+
+cat('##All output files')
+cat('\n\n')
+all_files = list.files(path = Sys.getenv('REPORT_FILES_PATH'), 
+                       full.names = TRUE, 
+                       recursive = TRUE)
+
+for (f in sub(Sys.getenv('REPORT_FILES_PATH'), '.', all_files) ) {
+  cat('* [', f, '](', f, ')\n')
+}
+cat('\n')
+```
+