From 38ec7a1db016a158f324b8dc2d7a8d4b4c816d3b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 28 Jul 2015 17:07:18 +0200
Subject: [PATCH] updating docs for flexiprep

---
 docs/pipelines/flexiprep.md | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/docs/pipelines/flexiprep.md b/docs/pipelines/flexiprep.md
index 613b53463..83d2dd6db 100644
--- a/docs/pipelines/flexiprep.md
+++ b/docs/pipelines/flexiprep.md
@@ -55,8 +55,8 @@ All other values should be provided in the config. Specific config values toward
 
 | Name | Type | Function |
 | ---- | ---- | -------- |
-| skiptrim | Boolean | Skip the trimming step |
-| skipclip | Boolean | Skip the clipping step |
+| skiptrim | Boolean | Default false, if true the trimming step is skipped |
+| skipclip | Boolean | Default false, if true the clipping step is skipped |
 
 ## Result files
 The results from this pipeline will be a fastq file.
@@ -139,5 +139,7 @@ The pipeline also outputs 2 Fastqc runs one before and one after quality control
 │   │   └── summary.txt
 │   └── mySample_01.R2.qc_fastqc.zip
 ├── mySample_01.R2.qc.fastq.gz
-└── mySample_01.R2.qc.fastq.gz.md5
+├── mySample_01.R2.qc.fastq.gz.md5
+└── report
+
 ~~~
-- 
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