From 01401aaee74dac39e0502688654ef02771a88cd7 Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Thu, 15 Nov 2018 17:07:29 +1100
Subject: test-tnpair: avoid gridss.call while it's broken
---
test-tnpair.nix | 1 -
1 file changed, 1 deletion(-)
diff --git a/test-tnpair.nix b/test-tnpair.nix
index a6ea163..0f6a441 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -54,7 +54,6 @@ 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