diff options
Diffstat (limited to 'tools/samtools-view.nix')
| -rw-r--r-- | tools/samtools-view.nix | 5 |
1 files changed, 3 insertions, 2 deletions
diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix index 35a3fcb..4d2bdc7 100644 --- a/tools/samtools-view.nix +++ b/tools/samtools-view.nix @@ -15,8 +15,9 @@ assert (matchFiletype "samtools-view" { bam = _: true; sam = _: true; cram = _: let outfmtR = if outfmt != null then (if builtins.typeOf outfmt == "string" then { "bam" = toBam; "cram" = toCram; "sam" = toSam; }."${outfmt}" else outfmt) input else input.filetype; fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref; - outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;}; -in stage { + outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } { filetype = outfmtR; }; +in +stage { name = "samtools-view"; buildInputs = with pkgs; [ samtools ]; buildCommand = '' |