From 1ff9422ec0ab086a97c4acab5c8f4d15c2026172 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 6 Mar 2019 13:18:41 +1100
Subject: api docs: init bowtie

---
 doc/tools-doc.nix | 1 +
 doc/tools.xml     | 1 +
 tools/bowtie.nix  | 7 +++++++
 3 files changed, 9 insertions(+)

diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix
index b2cd7ba..e510209 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 bowtie 'Bowtie aligner'
     docgen bwa 'BWA aligner'
     docgen strelka 'Strelka2 variant caller'
 
diff --git a/doc/tools.xml b/doc/tools.xml
index f23dfeb..6b76bf7 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="bowtie.xml" />
   <xi:include href="bwa.xml" />
   <xi:include href="strelka.xml" />
  </section>
diff --git a/tools/bowtie.nix b/tools/bowtie.nix
index a4439d3..df97d36 100644
--- a/tools/bowtie.nix
+++ b/tools/bowtie.nix
@@ -3,6 +3,13 @@
 with bionix;
 
 {
+  /* Align a sequence against a reference
+  Type: align :: {ref :: fasta, bamOutput :: bool, ...} -> {input1 :: fastq, input2 :: fastq} -> bam/sam
+  */
   align = callBionixE ./bowtie-align.nix;
+
+  /* Create a Bowtie index
+  Type: index :: {seed :: int, ...} -> fasta -> index
+  */
   index = callBionixE ./bowtie-index.nix;
 }
-- 
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