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authorl-d-s <distefano.l@wehi.edu.au>2019-05-30 13:14:19 +1000
committerl-d-s <distefano.l@wehi.edu.au>2019-05-30 13:14:19 +1000
commitae7f055db36fda71d28e58fd22ee6ffc25e01dee (patch)
tree03e98f7c3208f642fb325cb04503e065d623df70 /tools
parent867e68554307d45e102ba3267f5f469d02fc6a86 (diff)
parent1d83daa0794463ecfea4ea56fe6ef917fffcd7b0 (diff)
Merge branch 'add-picard' of mac2559:~/Projects/bionix
Diffstat (limited to 'tools')
-rw-r--r--tools/picard-markDuplicates.nix26
-rw-r--r--tools/picard.nix7
2 files changed, 33 insertions, 0 deletions
diff --git a/tools/picard-markDuplicates.nix b/tools/picard-markDuplicates.nix
new file mode 100644
index 0000000..aff1e32
--- /dev/null
+++ b/tools/picard-markDuplicates.nix
@@ -0,0 +1,26 @@
+{ bionix
+, flags ? null
+} :
+
+inputBam :
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "picard-markDuplicates" { bam = _: true; } input);
+assert (matchFileSorting "picard-markDuplicates" { coord = _: true; } input);
+
+stage {
+ name = "picard-markDuplicates";
+ buildInputs = with pkgs;
+ [ picard-tools ];
+ outputs = [ "out" "metrics" ];
+ buildCommand = ''
+ picard MarkDuplicates \
+ I=${inputBam} \
+ O=$out \
+ M=$metrics \
+ ${optionalString (flags != null) flags}
+ '';
+} \ No newline at end of file
diff --git a/tools/picard.nix b/tools/picard.nix
new file mode 100644
index 0000000..551995f
--- /dev/null
+++ b/tools/picard.nix
@@ -0,0 +1,7 @@
+{ bionix }:
+
+with bionix;
+
+{
+ markDuplicates = callBionixE ./picard-markDuplicates.nix;
+} \ No newline at end of file