From 0e2e1e2c432d597e477890297b9a29f743acb1b9 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Wed, 19 Dec 2018 16:45:08 +1100 Subject: gridss: simplify preprocessing and rewrite using new pipe function --- tools/gridss.nix | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) (limited to 'tools') diff --git a/tools/gridss.nix b/tools/gridss.nix index 009752e..5bb9484 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -17,6 +17,13 @@ rec { assemble = callBionixE ./gridss-assemble.nix; identifyVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify); annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate); - preprocessBam = input: with samtools; sort {} (gridss.softClipsToSplitReads {} (gridss.computeSamTags {} (sort {nameSort = true;} (gridss.extractSVReads {} (markdup {} (sort {} (fixmate {mateScore = true;} (sort {nameSort = true;} input)))))))); - call = inputs: bionix.gridss.annotateVariants {} (map gridss.preprocessBam inputs); + preprocessBam = with samtools; + pipe [ + (gridss.extractSVReads {}) + (sort {nameSort = true;}) + (gridss.computeSamTags {}) + (gridss.softClipsToSplitReads {}) + (sort {}) + ]; + call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs); } -- cgit v1.2.3