diff options
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/samtools-index.nix | 11 |
1 files changed, 7 insertions, 4 deletions
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix index d0f8d7a..62ee4c9 100644 --- a/tools/samtools-index.nix +++ b/tools/samtools-index.nix @@ -8,16 +8,19 @@ with bionix; with lib; with types; -assert (matchFiletype "samtools-index" { bam = _: true; } input); +assert (matchFiletype "samtools-index" { bam = _: true; cram = _: true; } input); assert (matchFileSorting "samtools-index" { coord = _: true; } input); +let + ext = matchFiletype "samtools-index-ext" { bam = _: "bam"; cram = _: "cram"; }; +in + stage { name = "samtools-index"; buildInputs = with pkgs; [ samtools ]; buildCommand = '' - ln -s ${input} input.bam - samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.bam - cp input.bam.bai $out + ln -s ${input} input.${ext input} + samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.${ext input} $out ''; passthru.multicore = true; } |