From 22e61f4fbdc0fc698a25fbe9aa64ebb4da1e32a8 Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Thu, 6 Jun 2019 09:33:36 +1000
Subject: picard-markDuplicates: fix input and output types

---
 tools/picard-markDuplicates.nix | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

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;
 }
-- 
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