diff options
Diffstat (limited to 'tools/bwa-mem.nix')
| -rw-r--r-- | tools/bwa-mem.nix | 3 |
1 files changed, 2 insertions, 1 deletions
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix index 52e73d1..84038d9 100644 --- a/tools/bwa-mem.nix +++ b/tools/bwa-mem.nix @@ -3,6 +3,7 @@ , bamOutput ? true , flags ? null , indexAttrs ? { } +, RG ? { } }: { input1 @@ -17,7 +18,6 @@ with compression; 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 { name = "bwa-mem"; @@ -33,6 +33,7 @@ stage { fi bwa mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \ ${optionalString (input2 != null) (fq input2)} \ + ${optionalString (RG ? ID) "-R'@RG\\t${concatMapAttrsStringsSep "\\t" (k: v: "${k}:${v}") RG}'"} \ ${optionalString bamOutput "| samtools view -b"} \ > $out ''; |