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| author | Justin Bedo <cu@cua0.org> | 2021-02-19 11:18:10 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2021-02-19 11:18:10 +1100 |
| commit | 64f8b0cb124445620b30e10e268fd7670ccb3189 (patch) | |
| tree | 8aba918a125ad0c780bf8ccb4c0e41b2ab91a7f9 /test-tnpair.nix | |
| parent | 834d736a00f5bd7155cb137d5a3e94e1413e8ada (diff) | |
samtools-index: support cram indexing
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 70fb5c8..7cc5453 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -64,6 +64,7 @@ let }; testNaming = linkOutputs { + crai = samtools.index {} (samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour); kallisto = kallisto.quant {inherit ref;} (attrValues tnpair.tumour.files); facets = facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}; cnvkit = cnvkitResults.cnvs; |