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-rw-r--r--tools/picard-markDuplicates.nix9
1 files changed, 6 insertions, 3 deletions
diff --git a/tools/picard-markDuplicates.nix b/tools/picard-markDuplicates.nix
index aff1e32..8906f9e 100644
--- a/tools/picard-markDuplicates.nix
+++ b/tools/picard-markDuplicates.nix
@@ -8,8 +8,11 @@ with bionix;
with lib;
with types;
-assert (matchFiletype "picard-markDuplicates" { bam = _: true; } input);
-assert (matchFileSorting "picard-markDuplicates" { coord = _: true; } input);
+assert (matchFiletype "picard-markDuplicates" { bam = _: 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);
stage {
name = "picard-markDuplicates";
@@ -23,4 +26,4 @@ stage {
M=$metrics \
${optionalString (flags != null) flags}
'';
-} \ No newline at end of file
+}