From 11b31bdad648c9af92ac6997303bc10849a7a2ef Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 2 May 2019 12:17:24 +1000
Subject: shard: Implement some basic sharding for FQ files

---
 default.nix     | 5 ++++-
 test-tnpair.nix | 5 +++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/default.nix b/default.nix
index d67f2eb..61f2974 100644
--- a/default.nix
+++ b/default.nix
@@ -68,9 +68,12 @@ let
     fetchFastQGZ = attrs: with types; tagFiletype (filetype.gz (filetype.fq {})) (fetchurl attrs);
     fetchFastAGZ = attrs: with types; tagFiletype (filetype.gz (filetype.fa {})) (fetchurl attrs);
 
+    # Turn a multi-output derivation into a list of derivations
+    outputDrvs = drv: map (o: lib.getAttr o drv) drv.outputs;
+
     # Export nixpkgs and standard library lib
     pkgs = nixpkgs;
-    lib = nixpkgs.lib // { types = types; };
+    lib = nixpkgs.lib // { types = types; shard = callBionix ./lib/shard.nix {};};
     stage = x@{ name, ... }: { multicore = false; } // nixpkgs.stdenvNoCC.mkDerivation (x // {name = "bionix-" + name;});
 
     # splitting/joining
diff --git a/test-tnpair.nix b/test-tnpair.nix
index f2e84ac..802a2bb 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -39,6 +39,10 @@ let
     variants = callVariants alignments;
     glvariants = strelka.call {} (builtins.attrValues alignments);
     platypusVars = platypus.call {} (builtins.attrValues alignments);
+    shards = pipe [
+      (shard.fastQPair 2)
+      (map (bwa.align {inherit ref;}))
+    ] normal.files;
   };
 
   tnpairResult = processPair tnpair;
@@ -56,6 +60,7 @@ let
     (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
     (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2")
     (ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3")
+    (ln (samtools.merge {} tnpairResult.shards) "alignments/merged-shards.bam")
     (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam")
     (ln (samtools.merge {} [(nameSort tnpairResult.alignments.tumour) (nameSort tnpairResult.alignments.normal)]) "alignments/merged-namesorted.bam")
     (ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)) "alignments/${tnpair.tumour.name}.cram")
-- 
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