diff options
| -rw-r--r-- | tools/picard-markDuplicates.nix | 6 |
1 files changed, 5 insertions, 1 deletions
diff --git a/tools/picard-markDuplicates.nix b/tools/picard-markDuplicates.nix index 6b15310..957a05e 100644 --- a/tools/picard-markDuplicates.nix +++ b/tools/picard-markDuplicates.nix @@ -9,7 +9,10 @@ with lib; with types; assert (matchFiletype "picard-markDuplicates" { bam = _: true; } inputBam); -assert !(matchFileSorting "picard-markDuplicates" { none = _: true; } inputBam); +assert (matchFileSorting + "picard-markDuplicates" + { coord = _: true; name = _: true; } + inputBam); # Note that picard markDuplicates has different behaviour depending on whether the input # is name-sorted or coordinate-sorted. @@ -26,4 +29,5 @@ stage { M=$metrics \ ${optionalString (flags != null) flags} ''; + passthru.filetype = inputBam.filetype; } |