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| author | Justin Bedo <cu@cua0.org> | 2018-10-04 12:06:54 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-10-04 12:06:54 +1000 |
| commit | fe68926931b280aaf29808566b49b2e704e8556a (patch) | |
| tree | dad0e9e11852e161c87ea6b7f4f6100a5180b9f2 /tools/mosdepth-depth.nix | |
| parent | 51f3817ecd2ad099b951d11e55eb3e2c516174d3 (diff) | |
Refactor to use bionix tree directly
Diffstat (limited to 'tools/mosdepth-depth.nix')
| -rw-r--r-- | tools/mosdepth-depth.nix | 14 |
1 files changed, 7 insertions, 7 deletions
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix index be28aaf..7043c43 100644 --- a/tools/mosdepth-depth.nix +++ b/tools/mosdepth-depth.nix @@ -1,10 +1,10 @@ -{ stdenv -, lib -, callPackage -, mosdepth -, index ? callPackage ./samtools-index.nix {} -, flags ? null}: +{ bionix +, nixpkgs +, indexAttrs ? {} +, flags ? null +}: +with nixpkgs; with lib; input: @@ -15,7 +15,7 @@ stdenv.mkDerivation { buildCommand = '' mkdir $out ln -s ${input} input.bam - ln -s ${index input} input.bam.bai + ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam ''; } |