cleanup examples and stray files

1 files changed, 26 insertions, 0 deletions

diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
new file mode 100644
index 0000000..2939db4
--- /dev/null
+++ b/examples/ex-tnpair/tnpair.nix
@@ -0,0 +1,26 @@
+# This is an example tumour-normal calling pipeline using strelka
+{ bionix ? import <bionix> {}
+, normal
+, tumour
+, ref
+}:
+
+with bionix;
+with lib;
+
+let
+  input = mapAttrs (_: fetchFastQGZ);
+
+  preprocess = pipe [
+    input
+    (bwa.align { ref = fetchFastA ref; })
+    (samtools.fixmate {})
+    (samtools.sort {})
+    (samtools.markdup {})
+  ];
+
+in linkDrv [
+  (ln (strelka.call {} {normal = preprocess normal; tumour = preprocess tumour;}) "strelka")
+  (ln (preprocess normal) "normal.bam")
+  (ln (preprocess tumour) "tumour.bam")
+]