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-rw-r--r--tools/octopus-call.nix37
-rw-r--r--tools/octopus-callSomatic.nix53
-rw-r--r--tools/octopus.nix8
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;
+}