diff options
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") |