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author | Justin Bedo <cu@cua0.org> | 2021-10-29 17:39:01 +1100 |
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committer | Justin Bedo <cu@cua0.org> | 2021-10-29 17:39:01 +1100 |
commit | bac9248a5e08e8afdf5485a6e27cfe72e1ca5090 (patch) | |
tree | 8719a280b56122017d46b582cd3da8547dd3f548 /tools/samtools-view.nix | |
parent | ab809b8c77efdad9fb54d3591a0193a1cbe888d1 (diff) |
treewide reformatting and simplification
- simplify with statix
- reformat with nixpkgs-fmt
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 = '' |