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{bionix}:
with bionix;
with lib;
rec {
jar = pkgs.fetchurl {
url = "https://github.com/PapenfussLab/gridss/releases/download/v2.11.1/gridss-2.11.1-gridss-jar-with-dependencies.jar";
sha256 = "sha256-x3+vdaNzEOhCQXSqmU6U3S2xUXy0SSdMle0QhiM2Qb8=";
};
/* 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 and convert soft clips to split reads
Type: preprocessBam :: bam -> bam
*/
preprocessBam = with samtools;
flip pipe [
(gridss.extractSVReads {})
(sort {nameSort = true;})
(gridss.computeSamTags {})
(gridss.softClipsToSplitReads {})
(sort {})
];
/* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual tools above.
Type: call :: [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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