From e7cd661d1c5fb4135e3d436e151294e26aef9127 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 29 Oct 2018 15:33:53 +1100
Subject: Split gridss into constituents

Wrap each individual command for GRIDSS so that bionix executed the pipeline
rather than GRIDSS. This patch introduces a "call" function that executed the
whole pipeline in bionix on an arbitrary BAM file.

Resolves #10.
---
 test-tnpair.nix | 1 +
 1 file changed, 1 insertion(+)

(limited to 'test-tnpair.nix')

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 0f6a441..a6ea163 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -54,6 +54,7 @@ let
       ln -s ${tnpairResult.variants} $out/strelka
       mkdir $out/alignments
       ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [tumour])} $out/gridss
+      ln -s ${gridss.call (with tnpairResult.alignments; [tumour])} $out/gridss2
       ln -s ${samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]} $out/alignments/merged.bam
       ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)} $out/alignments/${tnpair.tumour.name}.cram
       ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)} $out/alignments/${tnpair.normal.name}.cram
-- 
cgit v1.2.3