1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
|
{ bionix }:
with bionix;
with lib;
rec {
jar = pkgs.fetchurl {
url = "https://github.com/PapenfussLab/gridss/releases/download/v2.12.0/gridss-2.12.0-gridss-jar-with-dependencies.jar";
sha256 = "sha256-GLLA1pfGuN6xkvO9iALkifkNJhTBtbyCaWaKxDujRGc=";
};
/* 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);
}
|
