From ca3d5d1550d068b62dbc836b07abefc3bb06cab9 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 8 Oct 2018 14:22:50 +1100 Subject: Fix type in samtools-view --- tools/samtools-view.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/samtools-view.nix b/tools/samtools-view.nix index e1cdac1..b791534 100644 --- a/tools/samtools-view.nix +++ b/tools/samtools-view.nix @@ -11,12 +11,12 @@ with nixpkgs; with lib; with bionix.types; -assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: true; } input); +assert (matchFiletype "samtools-view" { bam = _: true; sam = _: true; cram = _: true; } input); let outfmtR = if outfmt != null then outfmt input else input.filetype; fa = ref: matchFiletype "samtools-view-ref" { fa = _: ref; } ref; - outfmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;}; + outfmtFlags = matchFiletype "samtools-view-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = x: "-O CRAM -T ${fa x.ref}"; } {filetype = outfmtR;}; in stdenv.mkDerivation { name = "samtools-view"; buildInputs = [ samtools ]; -- cgit v1.2.3