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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-11-29 09:47:14 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-11-29 11:24:37 +1100 |
| commit | 039b213f0a217f4787c04d40990006ee6d475173 (patch) | |
| tree | 6d9608fc9f611718ed62c40711371149c062f82a /test-tnpair.nix | |
| parent | c65b5e54d2afb94b671a41ea3d704d7ae101a50d (diff) | |
Revert "test-tnpair: avoid gridss.call while it's broken"
This reverts commit 01401aaee74dac39e0502688654ef02771a88cd7.
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 1 |
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 |