ampliconarchitect: init

1 files changed, 31 insertions, 0 deletions

diff --git a/tools/aa-call.nix b/tools/aa-call.nix
new file mode 100644
index 0000000..1c6a121
--- /dev/null
+++ b/tools/aa-call.nix
@@ -0,0 +1,31 @@
+{
+  bionix,
+  seeds,
+  license,
+  flags ? "",
+  downsample ? 0.1,
+  ...
+}: input:
+with bionix; let
+  indexedBam = linkOutputs {
+    "input.bam" = input;
+    "input.bam.bai" = samtools.index {} input;
+  };
+in
+  stage {
+    name = "aa-call";
+    MOSEKLM_LICENSE_FILE = license;
+    buildInputs = [bionix.ampliconarchitect.app];
+    buildCommand = ''
+      mkdir $out
+      export AA_DATA_REPO=$TMPDIR
+      tar -xzf ${self.aa.ref}
+      AmpliconArchitect.py \
+        --bam ${indexedBam}/input.bam \
+        --bed ${seeds} \
+        --ref GRCh38 \
+        --out $out/out \
+        --downsample ${toString downsample} \
+        $flags
+    '';
+  }