From 8fa9b007544a37b2674a2eb87978652e14fbd2b3 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 6 Mar 2019 13:31:04 +1100
Subject: api docs: init facets

---
 doc/tools-doc.nix | 1 +
 doc/tools.xml     | 1 +
 tools/ascat.nix   | 4 ++--
 tools/facets.nix  | 4 ++++
 4 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix
index a27cde9..5ee8e22 100644
--- a/doc/tools-doc.nix
+++ b/doc/tools-doc.nix
@@ -28,6 +28,7 @@ stage {
     docgen bowtie 'Bowtie aligner'
     docgen bwa 'BWA aligner'
     docgen cnvkit 'CNVkit CNV caller'
+    docgen facets 'Facets CNV caller'
     docgen strelka 'Strelka2 variant caller'
 
     mkdir $out
diff --git a/doc/tools.xml b/doc/tools.xml
index 8eb69ce..33a053b 100644
--- a/doc/tools.xml
+++ b/doc/tools.xml
@@ -12,6 +12,7 @@
   <xi:include href="bowtie.xml" />
   <xi:include href="bwa.xml" />
   <xi:include href="cnvkit.xml" />
+  <xi:include href="facets.xml" />
   <xi:include href="strelka.xml" />
  </section>
 </book>
diff --git a/tools/ascat.nix b/tools/ascat.nix
index 9e80e4a..700cb4e 100644
--- a/tools/ascat.nix
+++ b/tools/ascat.nix
@@ -6,12 +6,12 @@ with bionix;
   app = pkgs.callPackage ./ascat-app.nix {};
 
   /* Generate GC correction file for ascatNGS.
-  Type: {ref :: fasta, chrPrefix :: string, ...} -> (snps :: VCF) -> (gc :: GC)
+  Type: gccorrect :: {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
+  Type: callCNV :: {ref :: fasta, gc :: GC, ...} -> {tumour :: bam, normal :: bam, gender :: string} -> CNVs
   */
   callCNV = callBionixE ./ascat-callCNV.nix;
 }
diff --git a/tools/facets.nix b/tools/facets.nix
index ed10ffa..523c72a 100644
--- a/tools/facets.nix
+++ b/tools/facets.nix
@@ -4,5 +4,9 @@ with bionix;
 
 {
   app = lib.callPackageWith (pkgs // pkgs.rPackages) ./facets-app.nix {};
+
+  /* Call CNVs
+  Type: callCnv :: {...} -> {vcf, bams :: [bams]} -> CNVs
+  */
   callCNV = callBionix ./facets-call.nix;
 }
-- 
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