def generate(self, pflow, ct):
pflow.bundleScript("R/coverageTitrationPlots.R")
ctOuts = CoverageTitrationWorkflow().generate(pflow, ct)
flatCtOuts = listConcat(ctOuts.values())
ctSummaryRule = pflow.genRuleOnce(
"coverageTitrationSummaryAnalysis",
"Rscript --vanilla R/coverageTitrationPlots.R .")
bs = pflow.genBuildStatement(
["coverage-titration.csv", "coverage-titration.pdf"],
"coverageTitrationSummaryAnalysis", flatCtOuts)
def generate(self, pflow, ct):
pflow.bundleResource("scripts/R/ccsMappingPlots.R")
ccsMappingOutputs = CCSMappingWorkflow().generate(pflow, ct)
flatOutputs = listConcat(list(ccsMappingOutputs.values()))
ccsSummaryRule = pflow.genRuleOnce(
"ccsMappingSummaryAnalysis",
"Rscript --vanilla scripts/R/ccsMappingPlots.R .")
bs = pflow.genBuildStatement(["ccs-mapping.pdf"],
"ccsMappingSummaryAnalysis", flatOutputs)
def generate(self, pflow, ct):
pflow.bundleResource("scripts/R/coverageTitrationPlots.R")
ctOuts = CoverageTitrationWorkflow().generate(pflow, ct)
flatCtOuts = listConcat(list(ctOuts.values()))
ctSummaryRule = pflow.genRuleOnce(
"coverageTitrationSummaryAnalysis",
"Rscript --vanilla scripts/R/coverageTitrationPlots.R .")
bs = pflow.genBuildStatement(
[ "coverage-titration.csv", "coverage-titration.pdf"],
"coverageTitrationSummaryAnalysis",
flatCtOuts)
def generate(self, pflow, ct):
mapping = MappingWorkflow().generate(pflow, ct)
alignmentSets = {c: op.abspath(mapping[c][0]) for c in mapping}
flatMappingOuts = listConcat(list(mapping.values()))
generateConditionsJSON(pflow, ct, alignmentSets)
# run plots
for plotGroup in PLOTTING_GROUPS:
toolName = plotGroup
outputNonce = generateToolContract(pflow, toolName)
pbiPlotsRule = pflow.genRuleOnce(
toolName, "$grid " + PLOTTING_TOOLS_ROOT +
"/r/{toolName}.R run-rtc reports/{toolName}/rtc-{toolName}.json"
.format(toolName=toolName))
bs = pflow.genBuildStatement([outputNonce], toolName,
flatMappingOuts)
def generate(self, pflow, ct):
mapping = MappingWorkflow().generate(pflow, ct)
alignmentSets = { c : op.abspath(mapping[c][0]) for c in mapping }
flatMappingOuts = listConcat(list(mapping.values()))
generateConditionsJSON(pflow, ct, alignmentSets)
# run plots
for plotGroup in PLOTTING_GROUPS:
toolName = plotGroup
outputNonce = generateToolContract(pflow, toolName)
pbiPlotsRule = pflow.genRuleOnce(
toolName,
"$grid " + PLOTTING_TOOLS_ROOT + "/r/{toolName}.R run-rtc reports/{toolName}/rtc-{toolName}.json".format(toolName=toolName))
bs = pflow.genBuildStatement(
[ outputNonce ],
toolName,
flatMappingOuts)