diff options
| author | Justin Bedo <cu@cua0.org> | 2019-01-10 12:20:51 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-01-10 12:20:51 +1100 |
| commit | 9a70a25d6b7771df7ca53fcc34d61f582296e384 (patch) | |
| tree | 5de101f321f25fe48f4b3cbfd24103c5d84b8104 /test-tnpair.nix | |
| parent | 5cb6f6001ea3aefd52ebaf42c1714343d51a8822 (diff) | |
facets: init
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 0851a74..c531a83 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -35,11 +35,13 @@ let processPair = { tumour, normal }: rec { alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; }; variants = callVariants alignments; + platypusVars = platypus.call {} (builtins.attrValues alignments); }; tnpairResult = processPair tnpair; testNaming = linkDrv [ + (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets") (ln tnpairResult.variants "strelka") (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam") (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss") |