diff options
Diffstat (limited to 'tools/bwa-mem2.nix')
| -rw-r--r-- | tools/bwa-mem2.nix | 7 |
1 files changed, 4 insertions, 3 deletions
diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix index b16b7ea..843c5b0 100644 --- a/tools/bwa-mem2.nix +++ b/tools/bwa-mem2.nix @@ -2,7 +2,7 @@ , ref , bamOutput ? true , flags ? null -, indexAttrs ? {} +, indexAttrs ? { } }: { input1 @@ -18,7 +18,8 @@ let fa = f: matchFiletype "bwa-ref" { fa = _: f; } f; fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f; -in stage { +in +stage { name = "bwa-mem2"; buildInputs = with pkgs; [ bionix.bwa.app2 bc ] ++ optional bamOutput samtools; buildCommand = '' @@ -35,6 +36,6 @@ in stage { ${optionalString bamOutput "| samtools view -b"} \ > $out ''; - passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};}; + passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; }; passthru.multicore = true; } |