diff options
Diffstat (limited to 'tools/gridss-softClipsToSplitReads.nix')
-rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 9 |
1 files changed, 4 insertions, 5 deletions
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index c5d8062..315fbf9 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -1,5 +1,4 @@ { bionix -, nixpkgs , bwaIndexAttrs ? {} , faidxAttrs ? {} , alignerStreaming ? false @@ -9,9 +8,9 @@ }: -with nixpkgs; +with bionix; with lib; -with bionix.types; +with types; input: @@ -19,9 +18,9 @@ let ref = matchFiletype "gridss-softClipsToSplitReads" { bam = x: x.ref; } input; in -stdenv.mkDerivation rec { +stage rec { name = "gridss-softClipsToSplitReads"; - buildInputs = [ jre bwa ]; + buildInputs = with pkgs; [ jre bwa ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai |