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moleculeCoverageMI.snakefile
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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/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"],
mem=config["std_mem"],
runtime=config["std_runtime"],
pe=config["std_numCores"]
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 bxMol:
input:
lambda wildcards: getLRFullPath(config["samples"][wildcards.samples], config["bamFileName"])
output:
"results/bxMol/{samples}/{samples}.bxMol.{chr}.bed"
params:
bxTools=config["bxTools"],
samTools=config["samTools"],
mapQual=config["bx_mapQual"],
bedFile=config["bx_bedFileRoot"],
mem=config["std_mem"],
runtime=config["std_runtime"],
pe=config["std_numCores"]
log:
"logs/bxMol/{samples}/{samples}.bxMol.{chr}.log"
shell:
"{params.samTools} view -h -F 0x4 -q {params.mapQual} {input} {wildcards.chr} | {params.bxTools} mol - > {output} 2> {log}"
rule moleculeCoverageBXmol:
input:
expand("results/bxMol/{samples}/{samples}.bxMol.{chr}.bed", samples=config["samples"], chr=CHRS),
output:
corrDepth="results/moleculeCoverageBXmol/{tumor}/{tumor}.BXcounts.txt",
cna="results/moleculeCoverageBXmol/{tumor}/{tumor}.cna.seg",
segTxt="results/moleculeCoverageBXmol/{tumor}/{tumor}.seg.txt",
paramTxt="results/moleculeCoverageBXmol/{tumor}/{tumor}.params.txt",
params:
tumDir="results/bxMol/{tumor}/",
normDir=lambda wildcards: "results/bxMol/" + config["pairings"][wildcards.tumor] + "/",
outDir="results/moleculeCoverageBXmol/{tumor}/",
molCovScript=config["molCovBXMol_script"],
id="{tumor}",
minReadsPerBX=config["molCov_minReadsPerBX"],
minLengthMI=config["molCov_minLengthMI"],
maxLengthMI=config["molCov_maxLengthMI"],
genomeStyle=config["genomeStyle"],
chrs=config["molCov_chrs"],
maxCN=config["molCov_maxCN"],
gcwig=config["molCov_gcWig"],
mapwig=config["molCov_mapWig"],
titanLibDir=config["TitanCNA_libdir"],
ichorLibDir=config["ichorCNA_libdir"],
centromere=config["centromere"],
mem=config["std_mem"],
runtime=config["std_runtime"],
pe=config["std_numCores"]
log:
"logs/moleculeCoverageBXmol/{tumor}.molCov.log"
shell:
"Rscript {params.molCovScript} --id {params.id} --tumorBXDir {params.tumDir} --normalBXDir {params.normDir} --minReadsPerBX {params.minReadsPerBX} --minLengthMI {params.minLengthMI} --maxLengthMI {params.maxLengthMI} --genomeStyle {params.genomeStyle} --chrs \"{params.chrs}\" --maxCN {params.maxCN} --gcWig {params.gcwig} --libdirTitanCNA {params.titanLibDir} --libdirIchorCNA {params.ichorLibDir} --outDir {params.outDir} --centromere {params.centromere} > {log} 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"],
gcwig=config["molCov_gcWig"],
mapwig=config["molCov_mapWig"],
titanLibDir=config["TitanCNA_libdir"],
ichorLibDir=config["ichorCNA_libdir"],
centromere=config["centromere"],
mem=config["std_mem"],
runtime=config["std_runtime"],
pe=config["std_numCores"]
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} --gcWig {params.gcwig} --libdirTitanCNA {params.titanLibDir} --libdirIchorCNA {params.ichorLibDir} --outDir {params.outDir} --centromere {params.centromere} > {log} 2> {log}"