diff options
Diffstat (limited to 'tools/minimap2-align.nix')
| -rw-r--r-- | tools/minimap2-align.nix | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/tools/minimap2-align.nix b/tools/minimap2-align.nix index 18bca35..e7e71c6 100644 --- a/tools/minimap2-align.nix +++ b/tools/minimap2-align.nix @@ -3,6 +3,7 @@ , bamOutput ? true , flags ? null , preset +, RG ? { } }: { input1 @@ -30,6 +31,7 @@ stage { fi minimap2 ${optionalString (flags != null) flags} -t $cores -ax ${preset} 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 ''; |