diff options
| -rw-r--r-- | tools/picard-markDuplicates.nix | 6 |
1 files changed, 3 insertions, 3 deletions
diff --git a/tools/picard-markDuplicates.nix b/tools/picard-markDuplicates.nix index 8906f9e..6b15310 100644 --- a/tools/picard-markDuplicates.nix +++ b/tools/picard-markDuplicates.nix @@ -9,10 +9,10 @@ with lib; with types; assert (matchFiletype "picard-markDuplicates" { bam = _: true; } inputBam); +assert !(matchFileSorting "picard-markDuplicates" { none = _: true; } inputBam); -# Not sure what to do with sorting: behavior varies based on sortedness of input! -# See: https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates -# assert (matchFileSorting "picard-markDuplicates" { coord = _: true; } inputBam); +# Note that picard markDuplicates has different behaviour depending on whether the input +# is name-sorted or coordinate-sorted. stage { name = "picard-markDuplicates"; |