diff options
| author | Justin Bedo <cu@cua0.org> | 2018-09-27 21:13:35 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-09-28 07:54:22 +1000 |
| commit | 8df1eae273acaf97ead80b3f5ef78a387be0934b (patch) | |
| tree | 9b422f07843eaf85234e33ffe60f1efd9f83cc66 /tools | |
| parent | a75e95881c49cfa52cc47c27a4980b2381cc0fbf (diff) | |
Fix missing index for mosdepth
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/mosdepth-depth.nix | 6 |
1 files changed, 5 insertions, 1 deletions
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix index 586cdcb..be28aaf 100644 --- a/tools/mosdepth-depth.nix +++ b/tools/mosdepth-depth.nix @@ -1,6 +1,8 @@ { stdenv , lib +, callPackage , mosdepth +, index ? callPackage ./samtools-index.nix {} , flags ? null}: with lib; @@ -12,6 +14,8 @@ stdenv.mkDerivation { buildInputs = [ mosdepth ]; buildCommand = '' mkdir $out - mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out ${input} + ln -s ${input} input.bam + ln -s ${index input} input.bam.bai + mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam ''; } |