examples: added example tumour-normal calling pipeline script

9 files changed, 84 insertions, 0 deletions

diff --git a/example/call.nix b/examples/call.nix
index c9be673..c9be673 100644
--- a/example/call.nix
+++ b/examples/call.nix
diff --git a/example/default.nix b/examples/default.nix
index bceaa96..bceaa96 100644
--- a/example/default.nix
+++ b/examples/default.nix
diff --git a/example/ref.fa b/examples/ref.fa
index fdc51e6..fdc51e6 100644
--- a/example/ref.fa
+++ b/examples/ref.fa
diff --git a/example/sample1-1.fq b/examples/sample1-1.fq
index 743a5a8..743a5a8 100644
--- a/example/sample1-1.fq
+++ b/examples/sample1-1.fq
diff --git a/example/sample1-2.fq b/examples/sample1-2.fq
index aea7f3e..aea7f3e 100644
--- a/example/sample1-2.fq
+++ b/examples/sample1-2.fq
diff --git a/example/sample2-1.fq b/examples/sample2-1.fq
index a69ee45..a69ee45 100644
--- a/example/sample2-1.fq
+++ b/examples/sample2-1.fq
diff --git a/example/sample2-2.fq b/examples/sample2-2.fq
index a2bd3e3..a2bd3e3 100644
--- a/example/sample2-2.fq
+++ b/examples/sample2-2.fq
diff --git a/examples/tnpair b/examples/tnpair
new file mode 100755
index 0000000..5b84d5c
--- /dev/null
+++ b/examples/tnpair
@@ -0,0 +1,58 @@
+#!/bin/sh
+
+set -e
+
+if [[ $# -ne 5 ]] ; then
+    echo "Usage: $0 ref normal1 normal2 tumour1 tumour2"
+    exit 1
+fi
+
+function cleanup {
+    if [[ -e tnpair-$$ ]]; then
+        rm tnpair-$$
+    fi
+}
+trap cleanup INT TERM EXIT
+
+ref=`readlink -f $1`
+norm1=`readlink -f $2`
+norm2=`readlink -f $3`
+tumour1=`readlink -f $4`
+tumour2=`readlink -f $5`
+
+refhash=`nix-hash --base32 --type sha256 --flat $ref`
+norm1hash=`nix-hash --base32 --type sha256 --flat $norm1`
+norm2hash=`nix-hash --base32 --type sha256 --flat $norm2`
+tumour1hash=`nix-hash --base32 --type sha256 --flat $tumour1`
+tumour2hash=`nix-hash --base32 --type sha256 --flat $tumour2`
+
+cat > tnpair-$$ <<EOF
+import ./tnpair.nix {
+    normal = {
+        input1={
+            url="file://$norm1";
+            sha256="$norm1hash";
+        };
+        input2={
+            url="file://$norm2";
+            sha256="$norm2hash";
+        };
+    };
+    tumour = {
+        input1={
+            url = "file://$tumour1";
+            sha256 = "$tumour1hash";
+        };
+        input2={
+            url = "file://$tumour2";
+            sha256 = "$tumour2hash";
+        };
+    };
+    ref = {
+        url = "file://$ref";
+        sha256 = "$refhash";
+    };
+}
+EOF
+
+nix build --keep-going "(import ./tnpair-$$)"
diff --git a/examples/tnpair.nix b/examples/tnpair.nix
new file mode 100644
index 0000000..2939db4
--- /dev/null
+++ b/examples/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")
+]