diff options
Diffstat (limited to 'tools/gridss-callVariants.nix')
| -rw-r--r-- | tools/gridss-callVariants.nix | 20 |
1 files changed, 8 insertions, 12 deletions
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index 9d78896..e431560 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -1,15 +1,11 @@ -{ stdenv -, lib -, callPackage -, fetchurl -, jre -, R -, bwa +{ bionix +, nixpkgs , ref , blacklist ? null -, bwaIndex ? callPackage ./bwa-index.nix { inherit stdenv bwa lib; } -, faidx ? callPackage ./samtools-faidx.nix { inherit stdenv; } -, flags ? null}: +, bwaIndexAttrs ? {} +, faidxAttrs ? {} +, flags ? null +}: with lib; @@ -24,8 +20,8 @@ stdenv.mkDerivation rec { }; buildCommand = '' ln -s ${ref} ref.fa - ln -s ${faidx ref} ref.fa.fai - for f in ${bwaIndex ref}/*; do + ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai + for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do ln -s $f done mkdir $out |