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-rw-r--r--tools/picard-markDuplicates.nix6
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;
}