From 86b1b192501eecc8a4e566795327772c32b1633d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 5 Dec 2018 10:48:05 +1100
Subject: bowtie: init

---
 tools/bowtie-align.nix | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 tools/bowtie-align.nix

(limited to 'tools/bowtie-align.nix')

diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
new file mode 100644
index 0000000..456747a
--- /dev/null
+++ b/tools/bowtie-align.nix
@@ -0,0 +1,36 @@
+{ bionix
+, nixpkgs
+, ref
+, bamOutput ? true
+, flags ? null
+, indexAttrs ? {}
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+with bionix.compression;
+
+let
+  fa = f: matchFiletype "bowtie2-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f;
+
+in stdenv.mkDerivation {
+  name = "bowtie2-align";
+  buildInputs = [ bowtie2 bc ] ++ optional bamOutput samtools;
+  buildCommand = ''
+    cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
+    if [[ $cores -lt 1 ]] ; then
+      cores=1
+    fi
+    bowtie2 -x ${bionix.bowtie.index indexAttrs ref}/ref ${optionalString (flags != null) flags} --threads $cores \
+      ${if input2 != null then "-1 " + fq input1 + " -2 " + fq input2 else "-U " + fq input1} \
+      ${optionalString bamOutput "| samtools view -b"} \
+      > $out
+  '';
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+}
-- 
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