From f361afeab23a4e7b74e0f58bb64b142f6bc3652b Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 2 Jul 2019 16:02:54 +1000
Subject: CNVkit: split into multiple outputs

cnvkit: restructure out to link to multioutputs
---
 test-tnpair.nix        |  2 +-
 tools/cnvkit-batch.nix | 14 +++++++++++++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 7fe5750..701748d 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -51,7 +51,7 @@ let
 
   cnvkitResults = rec {
     cnvs = cnvkit.callCNV {} (with tnpairResult.alignments; { normals = [ normal ]; tumours = [ tumour ];});
-    plot = cnvkit.scatterPlot {} cnvs;
+    plot = cnvkit.scatterPlot {} cnvs.out1;
   };
 
   alignments = {
diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
index 5160867..113e0c9 100644
--- a/tools/cnvkit-batch.nix
+++ b/tools/cnvkit-batch.nix
@@ -23,6 +23,7 @@ assert (all sorted (normals ++ tumours));
 stage {
   name = "cnvkit";
   buildInputs = with pkgs; [ python3Packages.cnvkit ];
+  outputs = [ "out" ] ++ builtins.genList (x: "out${toString (x + 1)}") (length tumours);
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${samtools.faidx indexAttrs ref} ref.fa.fai
@@ -34,8 +35,19 @@ stage {
       -p $NIX_BUILD_CORES \
       -d $TMPDIR \
       ${optionalString (flags != null) flags}
+
+    # Copy individual tumour files
     mkdir $out
-    cp *.cn{r,s,n} $out
+    cnt=1
+    for f in ${concatStringsSep " " tumours} ; do
+      output="out$cnt"
+      mkdir ''${!output}
+      for g in $(basename $f)*.{cnr,cnn,cns} ; do
+        cp $g ''${!output}/sample-''${g#*-}
+      done
+      cnt=$((cnt+1))
+      ln -s ''${!output} $out/$output
+    done
   '';
   passthru.multicore = true;
 }
-- 
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