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| author | Justin Bedo <cu@cua0.org> | 2021-12-06 17:23:47 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2021-12-06 17:23:47 +1100 |
| commit | d75b723281aea944fbafdb28f5b0841a03827b4a (patch) | |
| tree | 1b3b8a6103ed6547d00b1e3e1b61b08038e08a27 /tools/bwa-mem2.nix | |
| parent | 18d442a951dc36a352c13c604642cb3d4db5a6b6 (diff) | |
parameterise RG line as nix attribute set
Allows more seamless transitioning between alingment algorithms
Diffstat (limited to 'tools/bwa-mem2.nix')
| -rw-r--r-- | tools/bwa-mem2.nix | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix index 843c5b0..e6237f0 100644 --- a/tools/bwa-mem2.nix +++ b/tools/bwa-mem2.nix @@ -3,6 +3,7 @@ , bamOutput ? true , flags ? null , indexAttrs ? { } +, RG ? { } }: { input1 @@ -33,6 +34,7 @@ stage { fi bwa-mem2 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 ''; |