From be9238d8266682925ae4ad4d291621c03ac38dfd Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 6 Mar 2019 13:25:52 +1100
Subject: api docs: init ascatNGS

---
 doc/tools-doc.nix | 1 +
 doc/tools.xml     | 1 +
 tools/ascat.nix   | 8 ++++++++
 3 files changed, 10 insertions(+)

diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix
index e510209..b79f69c 100644
--- a/doc/tools-doc.nix
+++ b/doc/tools-doc.nix
@@ -24,6 +24,7 @@ stage {
       nixdoc -c "$1" -d "$2" -f "$1.nix" | sed 's/lib\./bionix./g' |grep -v locations.xml > "$1.xml"
     }
 
+    docgen ascat 'ascatNGS CNV caller'
     docgen bowtie 'Bowtie aligner'
     docgen bwa 'BWA aligner'
     docgen strelka 'Strelka2 variant caller'
diff --git a/doc/tools.xml b/doc/tools.xml
index 6b76bf7..5a18670 100644
--- a/doc/tools.xml
+++ b/doc/tools.xml
@@ -8,6 +8,7 @@
           xmlns:xi="http://www.w3.org/2001/XInclude"
           xml:id="sec-tools">
   <title>Tools</title>
+  <xi:include href="ascat.xml" />
   <xi:include href="bowtie.xml" />
   <xi:include href="bwa.xml" />
   <xi:include href="strelka.xml" />
diff --git a/tools/ascat.nix b/tools/ascat.nix
index 05e2299..9e80e4a 100644
--- a/tools/ascat.nix
+++ b/tools/ascat.nix
@@ -4,6 +4,14 @@ with bionix;
 
 {
   app = pkgs.callPackage ./ascat-app.nix {};
+
+  /* Generate GC correction file for ascatNGS.
+  Type: {ref :: fasta, chrPrefix :: string, ...} -> (snps :: VCF) -> (gc :: GC)
+  */
   gccorrect = callBionixE ./ascat-gccorrect.nix;
+
+  /* Call CNVs using ascatNGS. Gender is a string as per ascatNGS docs (e.g., "XX").
+  Type: {ref :: fasta, gc :: GC, ...} -> {tumour :: bam, normal :: bam, gender :: string} -> CNVs
+  */
   callCNV = callBionixE ./ascat-callCNV.nix;
 }
-- 
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