From 0418c23f5d3bff108744d96d1075b0e76b580fdd Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 18 Dec 2018 14:05:19 +1100 Subject: qsub: refactor overriding --- tools/gridss.nix | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) (limited to 'tools/gridss.nix') diff --git a/tools/gridss.nix b/tools/gridss.nix index d47a669..009752e 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -8,15 +8,15 @@ rec { url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar"; sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k"; }; - gridssConfig = callBionix ./gridss-configFile.nix {}; - callVariants = callBionix ./gridss-callVariants.nix; - computeSamTags = callBionix ./gridss-computeSamTags.nix; - softClipsToSplitReads = callBionix ./gridss-softClipsToSplitReads.nix; - collectMetrics = callBionix ./gridss-collectMetrics.nix; - extractSVReads = callBionix ./gridss-extractSVReads.nix; - assemble = callBionix ./gridss-assemble.nix; - identifyVariants = attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify; - annotateVariants = attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate; + gridssConfig = callBionixE ./gridss-configFile.nix {}; + callVariants = callBionixE ./gridss-callVariants.nix; + computeSamTags = callBionixE ./gridss-computeSamTags.nix; + softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix; + collectMetrics = callBionixE ./gridss-collectMetrics.nix; + extractSVReads = callBionixE ./gridss-extractSVReads.nix; + 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); } -- cgit v1.2.3