diff options
| -rw-r--r-- | test-tnpair.nix | 6 |
1 files changed, 4 insertions, 2 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 8da1207..978370c 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -11,7 +11,7 @@ let ref = fetchfa ./examples/ref.fa; - alignWithRG = rg: x: nameSort (bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'"; } x); + alignWithRG = aligner: rg: x: nameSort (aligner { inherit ref; RG = { ID = rg; SM = rg; }; } x); sort = sambamba.sort { }; nameSort = sambamba.sort { nameSort = true; }; flagstat = samtools.flagstat { }; @@ -39,7 +39,9 @@ let }; processPair = { tumour, normal }: rec { - alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; }; + alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG bwa.align x.name x.files)))) { inherit normal tumour; }; + bowtie-alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG bowtie.align x.name x.files)))) { inherit normal tumour; }; + bwa2-alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG bwa.mem2 x.name x.files)))) { inherit normal tumour; }; variants = callVariants alignments; octopusSomatic = octopus.callSomatic { } { inherit (alignments) normal; tumours = [ alignments.tumour ]; }; glvariants = strelka.call { } (builtins.attrValues alignments); |