Update README.md

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README.md

@@ -93,7 +93,7 @@ Whilst this set of scripts has been tested on a cluster environment with a netwo
 My aim with this series of scripts / pipeline was to create a light weight system with minimal dependancies that would be accessible to the more novice user, so I chose to use SGE directly as the scheduler of jobs since this is the most light weight and easiest win from my current scripting base.  I fully acknowledge that [Bpipe](https://code.google.com/p/bpipe/) would also have been a good choice here.  Since SGE job submission already happens in shell wrappers it made most sense to simply extend that system.  Ultimately the best system for GATK pipeline creation is the Broads own [Queue](https://www.broadinstitute.org/gatk/guide/topic?name=queue) however as  a custom dialect of [Scala](https://en.wikipedia.org/wiki/Scala_%28programming_language%29) implementation is none trivial and is harder to grasp if you're not already somewhat familiar with Scala.
 
 ### Style considerations ###
-Contrary to the belief held by certain coding pedants backticks are [not deprecated](http://unix.stackexchange.com/questions/126927/have-backticks-i-e-cmd-in-sh-shells-been-deprecated) and are part of the POSIX standard, personally since was I first exposed to shell scripting in the 90s I actually prefer backticks, their good enough for the markdown I'm using in this document so there good enough for use in my code, I don't nest backticks so don't have any issues with nesting.  I also think that backticks are cleaner visually than the dollar parens `$()` paradigm particularly if you're new to shell scripting.  For this reason I'm also employing the use of the external `basename` and `dirname` mainly for clarity in showing how I assign values to variables as the combination of `$()` and bash string manipulation operations are the perfect storm of Perl-like "explosion in a punctuation factory" code which is hard to read. 
+Contrary to the belief held by certain coding pedants backticks are [not deprecated](http://unix.stackexchange.com/questions/126927/have-backticks-i-e-cmd-in-sh-shells-been-deprecated) and are part of the POSIX standard, personally since I was first exposed to shell scripting in the 90s I actually prefer backticks, their good enough for the markdown I'm using in this document so there good enough for use in my code, I don't nest backticks so don't have any issues with nesting.  I also think that backticks are cleaner visually than the dollar parens `$()` paradigm particularly if you're new to shell scripting.  For this reason I'm also employing the use of the external `basename` and `dirname` mainly for clarity in showing how I assign values to variables as the combination of `$()` and bash string manipulation operations are the perfect storm of Perl-like "explosion in a punctuation factory" code which is hard to read. 
 
 ## Roadmap ##
 Ultimately I plan to re-implement this whole workflow in Queue, time permitting.  MuTect 2.x is on the horizon, so I've resisted implementing version 1.x into in to the automated pipeline owing to its dependance on the UG like downstream sample preparation and the need for a unified realignment of samples.  When MuTect 2.x is released there will be an option in the automated pipeline to specify which pairs of samples should be sent down the path for joint tumour/normal calling as MuTect 2.x will use the current g.vcf HC sample preparation workflow.