From e4c0708d97949bb543e94ff5bdc558eb4c0c3dce Mon Sep 17 00:00:00 2001 From: l-d-s Date: Thu, 30 May 2019 16:57:20 +1000 Subject: picard-markDuplicates: Check for _any_ sorting of input --- tools/picard-markDuplicates.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'tools') 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"; -- cgit v1.2.3