From abb7760edbc301256db6fc50b5fd475175bd7606 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 6 Mar 2019 13:28:41 +1100
Subject: api docs: init CNVkit

---
 doc/tools-doc.nix | 1 +
 doc/tools.xml     | 1 +
 tools/cnvkit.nix  | 6 +++++-
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix
index b79f69c..a27cde9 100644
--- a/doc/tools-doc.nix
+++ b/doc/tools-doc.nix
@@ -27,6 +27,7 @@ stage {
     docgen ascat 'ascatNGS CNV caller'
     docgen bowtie 'Bowtie aligner'
     docgen bwa 'BWA aligner'
+    docgen cnvkit 'CNVkit CNV caller'
     docgen strelka 'Strelka2 variant caller'
 
     mkdir $out
diff --git a/doc/tools.xml b/doc/tools.xml
index 5a18670..8eb69ce 100644
--- a/doc/tools.xml
+++ b/doc/tools.xml
@@ -11,6 +11,7 @@
   <xi:include href="ascat.xml" />
   <xi:include href="bowtie.xml" />
   <xi:include href="bwa.xml" />
+  <xi:include href="cnvkit.xml" />
   <xi:include href="strelka.xml" />
  </section>
 </book>
diff --git a/tools/cnvkit.nix b/tools/cnvkit.nix
index 610b18c..2259bec 100644
--- a/tools/cnvkit.nix
+++ b/tools/cnvkit.nix
@@ -3,6 +3,10 @@
 with bionix;
 
 {
-app = lib.callPackageWith (pkgs // pkgs.pythonPackages) ./cnvkit-app.nix {};
+  app = lib.callPackageWith (pkgs // pkgs.pythonPackages) ./cnvkit-app.nix {};
+
+  /* Call CNVs
+  Type: callCNV :: {targets :: target file, annotations :: annotation file, ...} -> {normals :: [bam], tumours :: [bam]} -> CNVs
+  */
   callCNV = callBionixE ./cnvkit-batch.nix;
 }
-- 
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