e3.log.empty() # start with an empty log # Begin logging step = LogicalStep(e3, stepName) # Establish temporary and Permenant outputs sampleOf = step.declareGarbageFile('sampleOf_s' + reads, suffix='fastq') sampledStats = step.declareGarbageFile('sampledStats', suffix='txt') # The following 2 are bound together by the same nameKey: stepFile = step.declareTargetFile( 'validateRep' + repNo, suffix='html') # will become nonGalaxyOutput nonGalaxyOutput = e3.createOutFile('validateRep'+repNo,'nonGalaxyOutput', \ '%s_s'+reads+'_fastqc/fastqc_report', ext='html' ) # FAKING step.run() step._status = 'Running' step.declareLogFile() # Ensures that the logical step dir and log exist step.log.out("--- Beginning '" + stepName + "' [" + datetime.now().strftime("%Y-%m-%d %X (%A)") + '] ---') # For posterity e3.printPaths() # Outputs of sampling will be found in the named tmpDir dir, # NOTE: sampledStats could be /dev/null as it is not examined e3.log.out('\n# fastqStatsAndSubsample [unversioned]:') err = e3.runCmd('> some command', log=step.log) if err != 0: step.log.out('>>> Failure on some command.') step.fail()
runningLog = e3.declareLogFile() e3.log.empty() # start with an empty log # Begin logging step = LogicalStep(e3,stepName) # Establish temporary and Permenant outputs sampleOf = step.declareGarbageFile('sampleOf_s' + reads, suffix='fastq') sampledStats = step.declareGarbageFile('sampledStats', suffix='txt') # The following 2 are bound together by the same nameKey: stepFile = step.declareTargetFile('validateRep'+repNo, suffix='html') # will become nonGalaxyOutput nonGalaxyOutput = e3.createOutFile('validateRep'+repNo,'nonGalaxyOutput', \ '%s_s'+reads+'_fastqc/fastqc_report', ext='html' ) # FAKING step.run() step._status = 'Running' step.declareLogFile() # Ensures that the logical step dir and log exist step.log.out("--- Beginning '" + stepName + "' [" + datetime.now().strftime("%Y-%m-%d %X (%A)")+ '] ---') # For posterity e3.printPaths() # Outputs of sampling will be found in the named tmpDir dir, # NOTE: sampledStats could be /dev/null as it is not examined e3.log.out('\n# fastqStatsAndSubsample [unversioned]:') err = e3.runCmd('> some command',log=step.log) if err != 0: step.log.out('>>> Failure on some command.') step.fail()