Commit 1e4967ef authored by Holger Brandl's avatar Holger Brandl

added table of contents options to spin.R

parent 16d3abec
......@@ -15,6 +15,7 @@ Use knitr to spin R documents
Usage: spin.R [options] <r_script> [<quoted_script_args>]
Options:
--toc Add a table of contents
-c Cache results
-e Show Code
-w Show warnings
......@@ -100,7 +101,15 @@ opts_chunk$set(
width=200
)
knit2html(basename(rmdScript), header=cssHeader)
knitOptions <- c()
## optionally render toc
## see http://stackoverflow.com/questions/25872558/generating-a-table-of-contents-toc-when-using-knitrs-spin
if(spin_opts$toc){
knitOptions= c("toc", markdown::markdownHTMLOptions(TRUE))
}
knit2html(basename(rmdScript), header=cssHeader, options = knitOptions)
## also remove the .md and the .Rmd files
if(is.logical(keep_markdown_files) & !keep_markdown_files){
......
......@@ -26,7 +26,7 @@ spinsnip(){
echo "spining $tmpR..."
shift
spinr $tmpR $*
spinr -e $tmpR $*
# rm -r $(dirname $tmpR)
rm ${tmpR}
......
......@@ -136,8 +136,8 @@ export -f CountFastqGzReads
IndexBams(){
for bamFile in $1; do
sem -j5 -no-notice samtools index $bamFile;
for bamFile in $@; do
sem -j5 samtools index $bamFile;
done
sem -no-notice --wait
}
......
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