octopus: initial functions

3 files changed, 98 insertions, 0 deletions

diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
new file mode 100644
index 0000000..f88960c
--- /dev/null
+++ b/tools/octopus-call.nix
@@ -0,0 +1,37 @@
+{ bionix
+, faidxAttrs ? {}
+, indexAttrs ? {}
+, flags ? ""}:
+
+with bionix;
+with lib;
+with types;
+
+inputs:
+
+let
+  getref = f: matchFiletype "octopus-callSomatic" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f;
+  refs = map getref inputs;
+  ref = head refs;
+
+in
+
+assert (length (unique refs) == 1);
+
+stage {
+  name = "octopus-call";
+  buildInputs = with pkgs; [ octopus-caller ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${samtools.faidx faidxAttrs ref} ref.fai
+    ${concatMapStringsSep "\n" (i: ''
+      ln -s ${i} $(basename ${i}).bam
+      ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
+    '') inputs}
+    octopus -R ref.fa -I *.bam -o $out \
+      --threads=$NIX_BUILD_CORES \
+      ${flags}
+  '';
+  passthru.filtype = filetype.vcf {ref = ref;};
+  passthru.multicore = true;
+}
diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix
new file mode 100644
index 0000000..e1c7ce6
--- /dev/null
+++ b/tools/octopus-callSomatic.nix
@@ -0,0 +1,53 @@
+{ bionix
+, faidxAttrs ? {}
+, indexAttrs ? {}
+, flags ? ""}:
+
+with bionix;
+with lib;
+with types;
+
+{normal, tumours}:
+
+let
+  smScript = pkgs.writeText "smScript.awk" ''
+    /^@RG/{
+      for(i = 1; i <= NF; i++) {
+        n=split($i, fields, ":")
+        if(n == 2 && fields[1] == "SM"){
+          print fields[2]
+          exit
+        }
+      }
+    }
+  '';
+
+  inputs = [normal] ++ tumours;
+  getref = f: matchFiletype "octopus-callSomatic" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f;
+  refs = map getref inputs;
+  ref = head refs;
+
+in
+
+assert (length (unique refs) == 1);
+
+
+stage {
+  name = "octopus-callSomatic";
+  buildInputs = with pkgs; [ octopus-caller samtools ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    ln -s ${samtools.faidx faidxAttrs ref} ref.fai
+    ${concatMapStringsSep "\n" (i: ''
+      ln -s ${i} $(basename ${i}).bam
+      ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
+    '') inputs}
+    normal=$(samtools view -H ${normal} | awk -f ${smScript})
+    octopus -R ref.fa -I *.bam -o $out \
+      --threads=$NIX_BUILD_CORES \
+      -N $normal \
+      ${flags}
+  '';
+  passthru.filetype = filetype.vcf {ref = ref;};
+  passthru.multicore = true;
+}
diff --git a/tools/octopus.nix b/tools/octopus.nix
new file mode 100644
index 0000000..4d0c7f6
--- /dev/null
+++ b/tools/octopus.nix
@@ -0,0 +1,8 @@
+{ bionix }:
+
+with bionix;
+
+{
+  call = callBionixE ./octopus-call.nix;
+  callSomatic = callBionixE ./octopus-callSomatic.nix;
+}