diff options
Diffstat (limited to 'test-tnpair.nix')
-rw-r--r-- | test-tnpair.nix | 12 |
1 files changed, 10 insertions, 2 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index ef2af1b..77b5727 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -1,11 +1,19 @@ with (import <nixpkgs> {}); -with (import <bionix> {}); with lib; let + bionix = (import <bionix> {}).extend (self: super: { + bwa = super.bwa // { index = attrs: super.bwa.index ({ flags = "-a is" ; } // attrs); }; + }); + +in + +with bionix; + +let ref = ./example/ref.fa; alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; - sort = samtools.sort { }; + sort = samtools.sort {}; flagstat = samtools.flagstat {}; check = fastqc.check {}; callVariants = strelka.call { inherit ref; }; |