From dbe76116e2fa84e22740b139a1eab8217f130856 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 27 Apr 2020 09:46:48 +1000
Subject: octopus: parameterise max-genotypes and targets

---
 tools/octopus-call.nix        | 12 ++++++++++++
 tools/octopus-callSomatic.nix | 11 +++++++++++
 2 files changed, 23 insertions(+)

diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
index 57dd71f..ca0677e 100644
--- a/tools/octopus-call.nix
+++ b/tools/octopus-call.nix
@@ -1,8 +1,15 @@
 { bionix
+, fast ? false
+, very-fast ? false
+, max-genotypes ? null
+, targets ? null
 , faidxAttrs ? {}
 , indexAttrs ? {}
 , flags ? ""}:
 
+assert !fast || !very-fast;
+assert max-genotypes == null || max-genotypes > 0;
+
 with bionix;
 with lib;
 with types;
@@ -30,6 +37,11 @@ stage {
     '') inputs}
     octopus -R ref.fa -I *.bam -o $out \
       --threads=$NIX_BUILD_CORES \
+      ${optionalString fast "--fast"} \
+      ${optionalString very-fast "--very-fast"} \
+      ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
+      ${optionalString (targets != null) (if builtins.typeOf targets == "list" then "-T ${concatStringsSep "," targets}" else "-t ${targets}")} \
+      -N $normal \
       ${flags}
   '';
   passthru.filetype = filetype.vcf {ref = ref;};
diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix
index e1c7ce6..5c2ca90 100644
--- a/tools/octopus-callSomatic.nix
+++ b/tools/octopus-callSomatic.nix
@@ -1,8 +1,15 @@
 { bionix
+, fast ? false
+, very-fast ? false
+, max-genotypes ? null
+, targets ? null
 , faidxAttrs ? {}
 , indexAttrs ? {}
 , flags ? ""}:
 
+assert !fast || !very-fast;
+assert max-genotypes == null || max-genotypes > 0;
+
 with bionix;
 with lib;
 with types;
@@ -45,6 +52,10 @@ stage {
     normal=$(samtools view -H ${normal} | awk -f ${smScript})
     octopus -R ref.fa -I *.bam -o $out \
       --threads=$NIX_BUILD_CORES \
+      ${optionalString fast "--fast"} \
+      ${optionalString very-fast "--very-fast"} \
+      ${optionalString (max-genotypes != null) "--max-genotypes ${toString max-genotypes}"} \
+      ${optionalString (targets != null) (if builtins.typeOf targets == "list" then "-T ${concatStringsSep "," targets}" else "-t ${targets}")} \
       -N $normal \
       ${flags}
   '';
-- 
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