From fb1cf1c39109cdd0e76687e5788561407d01d629 Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Thu, 30 May 2019 15:09:30 +1000
Subject: Add picard-markDuplicates - need to handle sorting ambiguity.

---
 tools/picard-markDuplicates.nix | 9 ++++++---
 1 file 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
+}
-- 
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