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-rw-r--r--tools/gridss.nix7
1 files changed, 4 insertions, 3 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix
index b9c1282..1a51537 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -1,11 +1,12 @@
{bionix}:
with bionix;
+with lib;
rec {
jar = pkgs.fetchurl {
- url = "https://github.com/PapenfussLab/gridss/releases/download/v2.7.3/gridss-2.7.3-gridss-jar-with-dependencies.jar";
- sha256 = "0gzqilx7f7cjchkmsb2fn5vcx4pxvxdngwmsnwhhjr96pgsw0j9d";
+ url = "https://github.com/PapenfussLab/gridss/releases/download/v2.8.3/gridss-2.8.3-gridss-jar-with-dependencies.jar";
+ sha256 = "1qdbl3pl51v53rq2ab50mb00bxswi1njak1dcdwqbwbw2bm1r6rh";
};
/* Generate configuration file for GRIDSS. Takes attribute sets to GRIDSS ini style format.
@@ -60,7 +61,7 @@ rec {
Type: preprocessBam :: bam -> bam
*/
preprocessBam = with samtools;
- pipe [
+ flip pipe [
(gridss.extractSVReads {})
(sort {nameSort = true;})
(gridss.computeSamTags {})