From 92da3257c6867b6f54943e39345ab295703a30c4 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 15 Aug 2019 14:27:43 +1000
Subject: hisat2: init

---
 tools/hisat2-align.nix | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 tools/hisat2-align.nix

(limited to 'tools/hisat2-align.nix')

diff --git a/tools/hisat2-align.nix b/tools/hisat2-align.nix
new file mode 100644
index 0000000..277b499
--- /dev/null
+++ b/tools/hisat2-align.nix
@@ -0,0 +1,38 @@
+{ bionix
+, ref
+, bamOutput ? true
+, flags ? null
+, indexAttrs ? {}
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with bionix;
+with lib;
+with types;
+with compression;
+
+let
+  fa = f: matchFiletype "hisat2-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "hisat2-input" { fq = _: f; gz = matchFiletype' "hisat2-input" { fq = _: "<(gunzip < ${f})"; }; } f;
+
+in stage {
+  name = "hisat2-align";
+  buildInputs = with pkgs; [ hisat2 bc samtools ];
+  buildCommand = ''
+    ln -s ${fa ref} ref.fa
+    cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
+    if [[ $cores -lt 1 ]] ; then
+      cores=1
+    fi
+    hisat2 ${optionalString (flags != null) flags} -p $cores -x ${hisat2.index indexAttrs ref}/ \
+      ${if input2 != null then "-1 ${fq input1} -2 ${fq input2}" else "-U ${fq input1}"} \
+      ${optionalString bamOutput "| samtools view -b"} \
+      | 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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