ascat: init

1 files changed, 37 insertions, 0 deletions

diff --git a/tools/ascat-callCNV.nix b/tools/ascat-callCNV.nix
new file mode 100644
index 0000000..357ab8a
--- /dev/null
+++ b/tools/ascat-callCNV.nix
@@ -0,0 +1,37 @@
+{ bionix
+, ref
+, gc
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
+, flags ? null
+}:
+
+{tumour, normal, gender}:
+
+with bionix;
+with lib;
+with types;
+
+stage rec {
+  name = "ascat-callCNV";
+  buildInputs = with pkgs; [ ascat.app ];
+  buildCommand = ''
+    mkdir $out
+    ln -s ${tumour} tumour.bam
+    ln -s ${bionix.samtools.index bamIndexAttrs tumour} tumour.bai
+    ln -s ${normal} normal.bam
+    ln -s ${bionix.samtools.index bamIndexAttrs normal} normal.bai
+    ln -s ${ref} ref.fa
+    ln -s ${samtools.faidx indexAttrs ref} ref.fa.fai
+    ascat.pl \
+      -outdir $out \
+      -tumour tumour.bam \
+      -normal normal.bam \
+      -reference ref.fa \
+      -snp_gc ${gc} \
+      -gender ${gender} \
+      -genderChr Y \
+      -protocol WGS \
+      -cpus $NIX_BUILD_CORES
+  '';
+}