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| author | Justin Bedo <cu@cua0.org> | 2018-10-25 08:02:20 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-10-25 08:02:20 +1100 |
| commit | 99ee99c490cc109b78986181ee1be4ce1cd0c0ed (patch) | |
| tree | c909b5e3d151b6542b243c261593ad4a223132f2 /test-tnpair.nix | |
| parent | 92b4ea2ddac572f8bd830858132956829d92a734 (diff) | |
Improve type safety of samtools-merge
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 7deaf3b..0f6a441 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 ${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 ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat |