aboutsummaryrefslogtreecommitdiff
path: root/tools
diff options
context:
space:
mode:
Diffstat (limited to 'tools')
-rw-r--r--tools/mosdepth-depth.nix6
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
'';
}