-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathmoleculeCoverage.snakefile
82 lines (73 loc) · 3.75 KB
/
moleculeCoverage.snakefile
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
configfile: "config/config.yaml"
configfile: "config/samples.yaml"
CHRS = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chrX', 'chrY']
#CHRS = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,'X','Y']
import glob
def getLRFullPath(base, filename):
return glob.glob(''.join([base, "/*/outs/", filename]))
rule correctMolCov:
input:
expand("results/bxTile/{samples}/{samples}.bxTile.{chr}.bed", samples=config["samples"], chr=CHRS),
#expand("results/bxMol/{samples}/{samples}.bxMol.{chr}.bed", samples=config["samples"], chr=CHRS),
#expand("results/moleculeCoverage/{tumor}/{tumor}.cna.seg", tumor=config["pairings"]),
#expand("results/moleculeCoverage/{tumor}/{tumor}.seg.txt", tumor=config["pairings"]),
#expand("results/moleculeCoverage/{tumor}/{tumor}.params.txt", tumor=config["pairings"]),
expand("results/moleculeCoverage/{tumor}/{tumor}.BXcounts.txt", tumor=config["pairings"]),
expand("results/moleculeCoverage/{tumor}/{tumor}.cna.seg", tumor=config["pairings"])
#expand("results/bxTile/{samples}/", samples=config["samples"])
#expand("results/moleculeCoverageBXmol/{tumor}/{tumor}.BXcounts.txt", tumor=config["pairings"])
# rule mkdir:
# output:
# directory("results/bxTile/{samples}/")
# params:
# mem=config["std_mem"],
# runtime=config["std_runtime"],
# pe=config["std_numCores"]
# shell:
# "mkdir -p {output}"
rule bxTile:
input:
lambda wildcards: getLRFullPath(config["samples"][wildcards.samples], config["bamFileName"])
output:
"results/bxTile/{samples}/{samples}.bxTile.{chr}.bed"
params:
bxTools=config["bxTools"],
samTools=config["samTools"],
mapQual=config["bx_mapQual"],
bedFile=config["bx_bedFileRoot"]
log:
"logs/bxTile/{samples}/{samples}.bxTile.{chr}.log"
shell:
"{params.samTools} view -h -F 0x4 -q {params.mapQual} {input} {wildcards.chr} | {params.bxTools} tile - -b {params.bedFile}.{wildcards.chr}.bed > {output} 2> {log}"
rule moleculeCoverage:
input:
expand("results/bxTile/{samples}/{samples}.bxTile.{chr}.bed", samples=config["samples"], chr=CHRS),
#tumDir="results/bxTile/{tumor}/",
#normDir=lambda wildcards: "results/bxTile/" + config["pairings"][wildcards.tumor] + "/"
output:
corrDepth="results/moleculeCoverage/{tumor}/{tumor}.BXcounts.txt",
cna="results/moleculeCoverage/{tumor}/{tumor}.cna.seg",
segTxt="results/moleculeCoverage/{tumor}/{tumor}.seg.txt",
paramTxt="results/moleculeCoverage/{tumor}/{tumor}.params.txt",
#outDir="results/moleculeCoverage/{tumor}/",
params:
tumDir="results/bxTile/{tumor}/",
normDir=lambda wildcards: "results/bxTile/" + config["pairings"][wildcards.tumor] + "/",
outDir="results/moleculeCoverage/{tumor}/",
molCovScript=config["molCov_script"],
id="{tumor}",
minReadsPerBX=config["molCov_minReadsPerBX"],
genomeStyle=config["genomeStyle"],
chrs=config["molCov_chrs"],
maxCN=config["molCov_maxCN"],
likModel=config["molCov_likModel"],
gcwig=config["molCov_gcWig"],
mapwig=config["molCov_mapWig"],
reptimewig=config["molCov_repTimeWig"],
titanLibDir=config["TitanCNA_libdir"],
ichorLibDir=config["ichorCNA_libdir"],
centromere=config["centromere"]
log:
"logs/moleculeCoverage/{tumor}.molCov.log"
shell:
"Rscript {params.molCovScript} --id {params.id} --tumorBXDir {params.tumDir} --normalBXDir {params.normDir} --minReadsPerBX {params.minReadsPerBX} --genomeStyle {params.genomeStyle} --chrs \"{params.chrs}\" --maxCN {params.maxCN} --likModel {params.likModel} --gcWig {params.gcwig} --mapWig {params.mapwig} --repTimeWig {params.reptimewig} --libdirTitanCNA {params.titanLibDir} --libdirIchorCNA {params.ichorLibDir} --outDir {params.outDir} --centromere {params.centromere} > {log} 2> {log}"