From 0c09091762accf8716ef7853dded34e1c86497aa Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 17 Apr 2019 19:06:00 +1000
Subject: snap: init

---
 tools/snap-align.nix | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 tools/snap-align.nix

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

diff --git a/tools/snap-align.nix b/tools/snap-align.nix
new file mode 100644
index 0000000..4647142
--- /dev/null
+++ b/tools/snap-align.nix
@@ -0,0 +1,37 @@
+{ bionix
+, ref
+, bamOutput ? true
+, flags ? null
+, indexAttrs ? {}
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with bionix;
+with lib;
+with types;
+with compression;
+
+let
+  fa = f: matchFiletype "snap-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "snap-input" { fq = _: f; gz = matchFiletype' "snap-input" { fq = _: f; }; } f;
+
+in stage {
+  name = "snap-align";
+  buildInputs = with pkgs; [ bionix.snap.app bc ] ++ optional bamOutput samtools;
+  buildCommand = ''
+    for f in /* ; do
+      ln -s $f
+    done
+    snap-aligner ${if input2 == null then "single" else "paired"} ${bionix.snap.index indexAttrs ref} ${fq input1} \
+      ${optionalString (input2 != null) (fq input2)} \
+      -o ${if bamOutput then "-bam" else "-sam" } - \
+      -t $NIX_BUILD_CORES \
+      ${optionalString (flags != null) flags} \
+      | samtools sort -n > $out
+  '';
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.multicore = true;
+}
-- 
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