diff options
Diffstat (limited to 'tools/gridss-callVariants.nix')
-rw-r--r-- | tools/gridss-callVariants.nix | 13 |
1 files changed, 11 insertions, 2 deletions
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index c313c3f..799c930 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -1,16 +1,25 @@ { bionix , nixpkgs -, ref , blacklist ? null , bwaIndexAttrs ? {} , faidxAttrs ? {} , flags ? null }: +with nixpkgs; with lib; +with bionix.types; inputs: +let + getref = matchFiletype "gridss-callVariants" { bam = x: x.ref; }; + refs = map getref inputs; + ref = head refs; +in + +assert (length (unique refs) == 1); + stdenv.mkDerivation rec { name = "gridss-callVariants"; buildInputs = [ jre R bwa ]; @@ -19,7 +28,7 @@ stdenv.mkDerivation rec { sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k"; }; buildCommand = '' - ln -s ${ref.seq} ref.fa + ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do ln -s $f |