diff options
Diffstat (limited to 'tools/sambamba-generic.nix')
-rw-r--r-- | tools/sambamba-generic.nix | 28 |
1 files changed, 28 insertions, 0 deletions
diff --git a/tools/sambamba-generic.nix b/tools/sambamba-generic.nix new file mode 100644 index 0000000..a6be65c --- /dev/null +++ b/tools/sambamba-generic.nix @@ -0,0 +1,28 @@ +{ bionix +, flags ? null +, tool +, region ? null +}: + +input: + +with bionix; +with lib; + +let + inherit (bionix.types) matchFiletype coordSort matchFileSorting; +in + +assert (matchFiletype "sambamba-${tool}" { bam = _: true; } input); + +stage { + name = "sambamba-${tool}"; + buildInputs = [ pkgs.sambamba ]; + buildCommand = '' + sambamba ${tool} -t $NIX_BUILD_CORES \ + ${optionalString (flags != null) flags} \ + ${if tool == "merge" then "$out ${concatStringsSep " " input}" else if tool == "slice" then "${input} ${region} > $out" else if tool == "flagstat" then "${input} > $out" else "${input} $out"} + ''; + passthru.filetype = if tool == "flagstat" || tool == "index" then null else if tool == "merge" then (head input).filetype else input.filetype; + passthru.multicore = true; +} |