Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat

diff rmarkdown_samtools_flagstat.Rmd @ 5:1c16536c70f5 draft

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author mingchen0919
date Wed, 27 Dec 2017 15:20:55 -0500
parents ec39bfeaf496
children
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--- a/rmarkdown_samtools_flagstat.Rmd	Wed Dec 27 15:14:47 2017 -0500
+++ b/rmarkdown_samtools_flagstat.Rmd	Wed Dec 27 15:20:55 2017 -0500
@@ -16,7 +16,7 @@
 ```
 
 
-# Reads alignment stats
+# Reads alignment stats on `r opt$input_bam_name`
 
 ```{r 'flagstat'}
 command = paste0('samtools flagstat ', opt$input_bam, ' > ', paste0(opt$report_dir, '/report.txt'))