From 0beb96d76c36598994a0f883010cc0770862ee2d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 31 Mar 2020 13:38:58 +0200
Subject: [PATCH] update inputs

---
 docs/pairedCnvCalling-inputs.md | 25 +++++--------------------
 1 file changed, 5 insertions(+), 20 deletions(-)

diff --git a/docs/pairedCnvCalling-inputs.md b/docs/pairedCnvCalling-inputs.md
index d8bc45f..19dffa4 100644
--- a/docs/pairedCnvCalling-inputs.md
+++ b/docs/pairedCnvCalling-inputs.md
@@ -171,11 +171,6 @@ PairedCnvCalling.
     <i>String </i><i>&mdash; Default:</i> <code>"32G"</code><br />
     The amount of memory this job will use.
 </dd>
-<dt id="PairedCnvCalling.caseSample.plotDenoisedCopyRatios.minimumContigLength"><a href="#PairedCnvCalling.caseSample.plotDenoisedCopyRatios.minimumContigLength">PairedCnvCalling.caseSample.plotDenoisedCopyRatios.minimumContigLength</a></dt>
-<dd>
-    <i>Int? </i><br />
-    The minimum length for a contig to be included in the plots.
-</dd>
 <dt id="PairedCnvCalling.caseSample.plotModeledSegments.javaXmx"><a href="#PairedCnvCalling.caseSample.plotModeledSegments.javaXmx">PairedCnvCalling.caseSample.plotModeledSegments.javaXmx</a></dt>
 <dd>
     <i>String </i><i>&mdash; Default:</i> <code>"7G"</code><br />
@@ -186,11 +181,6 @@ PairedCnvCalling.
     <i>String </i><i>&mdash; Default:</i> <code>"21G"</code><br />
     The amount of memory this job will use.
 </dd>
-<dt id="PairedCnvCalling.caseSample.plotModeledSegments.minimumContigLength"><a href="#PairedCnvCalling.caseSample.plotModeledSegments.minimumContigLength">PairedCnvCalling.caseSample.plotModeledSegments.minimumContigLength</a></dt>
-<dd>
-    <i>Int? </i><br />
-    The minimum length for a contig to be included in the plots.
-</dd>
 <dt id="PairedCnvCalling.controlSample.callCopyRatioSegments.javaXmx"><a href="#PairedCnvCalling.controlSample.callCopyRatioSegments.javaXmx">PairedCnvCalling.controlSample.callCopyRatioSegments.javaXmx</a></dt>
 <dd>
     <i>String </i><i>&mdash; Default:</i> <code>"6G"</code><br />
@@ -266,11 +256,6 @@ PairedCnvCalling.
     <i>String </i><i>&mdash; Default:</i> <code>"32G"</code><br />
     The amount of memory this job will use.
 </dd>
-<dt id="PairedCnvCalling.controlSample.plotDenoisedCopyRatios.minimumContigLength"><a href="#PairedCnvCalling.controlSample.plotDenoisedCopyRatios.minimumContigLength">PairedCnvCalling.controlSample.plotDenoisedCopyRatios.minimumContigLength</a></dt>
-<dd>
-    <i>Int? </i><br />
-    The minimum length for a contig to be included in the plots.
-</dd>
 <dt id="PairedCnvCalling.controlSample.plotModeledSegments.javaXmx"><a href="#PairedCnvCalling.controlSample.plotModeledSegments.javaXmx">PairedCnvCalling.controlSample.plotModeledSegments.javaXmx</a></dt>
 <dd>
     <i>String </i><i>&mdash; Default:</i> <code>"7G"</code><br />
@@ -281,16 +266,16 @@ PairedCnvCalling.
     <i>String </i><i>&mdash; Default:</i> <code>"21G"</code><br />
     The amount of memory this job will use.
 </dd>
-<dt id="PairedCnvCalling.controlSample.plotModeledSegments.minimumContigLength"><a href="#PairedCnvCalling.controlSample.plotModeledSegments.minimumContigLength">PairedCnvCalling.controlSample.plotModeledSegments.minimumContigLength</a></dt>
-<dd>
-    <i>Int? </i><br />
-    The minimum length for a contig to be included in the plots.
-</dd>
 <dt id="PairedCnvCalling.dockerImages"><a href="#PairedCnvCalling.dockerImages">PairedCnvCalling.dockerImages</a></dt>
 <dd>
     <i>Map[String,String] </i><i>&mdash; Default:</i> <code>{"gatk": "broadinstitute/gatk:4.1.4.0"}</code><br />
     The docker images used. Changing this may result in errors which the developers may choose not to address.
 </dd>
+<dt id="PairedCnvCalling.minimumContigLength"><a href="#PairedCnvCalling.minimumContigLength">PairedCnvCalling.minimumContigLength</a></dt>
+<dd>
+    <i>Int? </i><br />
+    The minimum length for a contig to be included in the plots.
+</dd>
 </dl>
 </details>