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{ bionix }:
with bionix;
with lib;
rec {
jar = pkgs.fetchurl {
url = "https://github.com/PapenfussLab/gridss/releases/download/v2.12.2/gridss-2.12.2-gridss-jar-with-dependencies.jar";
sha256 = "sha256-JlGFYs2ZJMa2TbCnM3yP10X/G5Fqqe5w4tdKzj7DHzM=";
};
/* Generate configuration file for GRIDSS. Takes attribute sets to GRIDSS ini style format.
Type: genConfig :: attrSet -> ini file
*/
genConfig = callBionix ./gridss-configFile.nix { };
/* Invoke the callVariants tool
Type: callVariants :: {blacklist :: drv = null, config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> variants
*/
callVariants = callBionixE ./gridss-callVariants.nix;
/* Invoke computeSamTags tool
Type: computeSamTags :: {config :: ini = null, heapSize :: String = "1G", ...} -> bam -> bam
*/
computeSamTags = callBionixE ./gridss-computeSamTags.nix;
/* Invoke softClipsToSplitReads tool
Type: softClipsToSplitReads :: {alignerStreaming :: Bool = false, config :: ini = null, heapSize :: String = "2G", ...} -> bam -> bam
*/
softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix;
/* Invoke collectMetrics tool
Type: collectMetrics :: {thresholdCoverage :: Int = 10000, config :: ini = null, heapSize :: String = "1G", ...} -> bam -> metrics
*/
collectMetrics = callBionixE ./gridss-collectMetrics.nix;
/* Invoke extractSVReads tool
Type: extractSVReads :: {unmappedReads :: Bool = false, minClipLength :: Int = 5, config :: ini = null, ...} -> bam -> bam
*/
extractSVReads = callBionixE ./gridss-extractSVReads.nix;
/* Invoke assembly tool
Type: assemble :: {config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> bam
*/
assemble = callBionixE ./gridss-assemble.nix;
shardedAssemble = n: a: input:
let
assemblies = genList
(i:
bionix.gridss.assemble
(a // {
jobNodes = n;
jobIndex = i;
})
input)
n;
in
if n <= 1 then
bionix.gridss.assemble a input
else
bionix.gridss.assemble (a // { workdirs = map (a: a.work) assemblies; })
input;
/* Invoke identifyVariants tool
Type: identifyVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
*/
identifyVariants = exec
(attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify);
/* Invoke annotateVariants tool
Type: annotateVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
*/
annotateVariants = exec
(attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate);
# As annotateVariants except include assembly in output
annotateAndAssemble = exec (attrs: input:
((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble);
/* Preprocess BAM files to extract SV reads
Type: preprocessBam :: bam -> bam
*/
preprocessBam = with samtools;
flip pipe [
(gridss.extractSVReads { })
(sort { nameSort = true; })
(gridss.computeSamTags { })
(sort { })
];
/* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual above tools.
Type: [bam] -> GRIDSS result
*/
call = inputs: gridss.annotateVariants { } (map gridss.preprocessBam inputs);
# As call but include assemblies in output
callAndAssemble = inputs:
gridss.annotateAndAssemble { } (map gridss.preprocessBam inputs);
}
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