From 20050d08b1d6b18f437d7ac44a4720f2c24d7f53 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 7 Feb 2022 14:37:43 +1100
Subject: pizzly: init

---
 tools/pizzly-call.nix | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 tools/pizzly-call.nix

(limited to 'tools/pizzly-call.nix')

diff --git a/tools/pizzly-call.nix b/tools/pizzly-call.nix
new file mode 100644
index 0000000..72e23bf
--- /dev/null
+++ b/tools/pizzly-call.nix
@@ -0,0 +1,24 @@
+{ bionix, kmerSize ? 31, gtf, cdna, alignScore ? 2, maxInsertSize ? 400 }:
+
+with bionix;
+with pkgs;
+
+input:
+stage {
+  name = "pizzly";
+  buildInputs = [ bionix.pizzly.app ];
+  buildCommand = ''
+    ln -s ${gtf} ref.gtf
+    ln -s ${cdna} ref.fa
+    mkdir $out
+    pizzly                          \
+      -G ref.gtf                    \
+      -C cache                      \
+      -F ref.fa                     \
+      -k ${toString kmerSize}       \
+      -o $out/output                \
+      -a ${toString alignScore}     \
+      -i ${toString maxInsertSize}  \
+      ${input}/fusion.txt
+  '';
+}
-- 
cgit v1.2.3