From 7611c8798f41427c5b48a3406d8bb9e0cde9786c Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Sat, 27 Jun 2020 14:35:30 +1000
Subject: octopus: write evidence bams to multioutput

---
 tools/octopus-call.nix        | 3 +++
 tools/octopus-callSomatic.nix | 3 +++
 2 files changed, 6 insertions(+)

(limited to 'tools')

diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix
index 1688d88..f33d87c 100644
--- a/tools/octopus-call.nix
+++ b/tools/octopus-call.nix
@@ -28,6 +28,7 @@ assert (length (unique refs) == 1);
 stage {
   name = "octopus-call";
   buildInputs = with pkgs; [ octopus-caller ];
+  outputs = [ "out" "evidence" ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${samtools.faidx faidxAttrs ref} ref.fai
@@ -35,7 +36,9 @@ stage {
       ln -s ${i} $(basename ${i}).bam
       ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
     '') inputs}
+    ${optionalString (length inputs > 1) "mkdir $evidence"}
     octopus -R ref.fa -I *.bam -o $out \
+      --bamout $evidence \
       --threads=$NIX_BUILD_CORES \
       ${optionalString fast "--fast"} \
       ${optionalString very-fast "--very-fast"} \
diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix
index 5c2ca90..d3e7f96 100644
--- a/tools/octopus-callSomatic.nix
+++ b/tools/octopus-callSomatic.nix
@@ -42,6 +42,7 @@ assert (length (unique refs) == 1);
 stage {
   name = "octopus-callSomatic";
   buildInputs = with pkgs; [ octopus-caller samtools ];
+  outputs = [ "out" "evidence" ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${samtools.faidx faidxAttrs ref} ref.fai
@@ -50,7 +51,9 @@ stage {
       ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai
     '') inputs}
     normal=$(samtools view -H ${normal} | awk -f ${smScript})
+    mkdir $evidence
     octopus -R ref.fa -I *.bam -o $out \
+      --bamout $evidence \
       --threads=$NIX_BUILD_CORES \
       ${optionalString fast "--fast"} \
       ${optionalString very-fast "--very-fast"} \
-- 
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