From cfee098a46e5b29dceba0f2a97d6e5ce914afc99 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 19 Jun 2014 11:02:04 +0200
Subject: [PATCH] Readme changed to README.md

---
 flexiprep/README.md | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/flexiprep/README.md b/flexiprep/README.md
index f94f0fcbe..bcfc9c7a3 100644
--- a/flexiprep/README.md
+++ b/flexiprep/README.md
@@ -3,14 +3,18 @@
 QC pipeline for fastq files
 
 ### Commandline options
-| Argument | Explain |
-| :- | :- |
-| -R1,--input_r1 <input_r1> | R1 fastq file (gzipped allowed) |
-| -outputDir,--outputdir <outputdir> | Output directory |
-| -config,--configfiles <configfiles> | Config Json file |
-| -R2,--input_r2 <input_r2> | R2 fastq file (gzipped allowed) |
-| -skiptrim,--skiptrim | Skip Trim fastq files |
-| -skipclip,--skipclip | Skip Clip fastq files |
+- -R1,--input_r1 <input_r1>
+-- R1 fastq file (gzipped allowed)
+- -outputDir,--outputdir <outputdir>
+-- Output directory
+- -config,--configfiles <configfiles>
+-- Config Json file
+- -R2,--input_r2 <input_r2>
+-- R2 fastq file (gzipped allowed)
+- -skiptrim,--skiptrim
+-- Skip Trim fastq files
+- -skipclip,--skipclip
+-- Skip Clip fastq files
 ---
 ### Config options
 
@@ -44,6 +48,6 @@ This can be used in the root of the config or within the flexiprep, within flexi
 | sickle | qualitytype | String |  |  |
 | sickle | defaultqualitytype | String | sanger | use this when quality type can't be found at fastqc |
 ---
-##License
+## License
 
 A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL license; For commercial users or users who do not want to follow the AGPL license, please contact sasc@lumc.nl to purchase a separate license.
-- 
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