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authorl-d-s <distefano.l@wehi.edu.au>2018-11-29 09:47:14 +1100
committerl-d-s <distefano.l@wehi.edu.au>2018-11-29 11:24:37 +1100
commit039b213f0a217f4787c04d40990006ee6d475173 (patch)
tree6d9608fc9f611718ed62c40711371149c062f82a
parentc65b5e54d2afb94b671a41ea3d704d7ae101a50d (diff)
Revert "test-tnpair: avoid gridss.call while it's broken"
This reverts commit 01401aaee74dac39e0502688654ef02771a88cd7.
-rw-r--r--test-tnpair.nix1
1 files changed, 1 insertions, 0 deletions
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