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| author | Justin Bedo <cu@cua0.org> | 2022-02-09 13:02:54 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2022-02-09 13:02:54 +1100 |
| commit | 6664d56a18be8f0e9f027d6e5723b4b4e35f2694 (patch) | |
| tree | 818359873b6893c7007311265eda6febd664ac2c | |
| parent | 25515012d0051a4074de0e4692b7fd336c7ddf4a (diff) | |
whisper: RG line support
| -rw-r--r-- | tools/whisper-align.nix | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/tools/whisper-align.nix b/tools/whisper-align.nix index 38bcedf..b6130bc 100644 --- a/tools/whisper-align.nix +++ b/tools/whisper-align.nix @@ -2,6 +2,7 @@ , ref , bamOutput ? true , flags ? null +, RG ? { } , indexAttrs ? { } }: @@ -33,6 +34,7 @@ stage { -stdout \ index ${fq input1} \ ${optionalString (input2 != null) (fq input2)} \ + ${optionalString (RG ? ID) "-rg '@RG\\t${concatMapAttrsStringsSep "\\t" (k: v: "${k}:${v}") RG}'"} \ > $out ''; passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.none { }; }; |