# Set up 'ana' so she can do all the work. If anaId matches another, then it's log is extended ana = GalaxyAnalysis(settingsFile, anaId, genome, expType) if testOnly: ana.dryRun = testOnly # What step expects: # # Inputs: 1 fastq file, pre-registered in the analysis keyed as: 'tags' + suffix + '.fastq' # Outputs: directory of files (will include html target) keyed as: 'fastqValDir' + suffix # zipped file of that directory keyed as: 'fastqVal' + suffix + '.zip' # html file in that directory keyed as: 'fastqVal' + suffix + '.html' # json file keyed as: 'fastqVal' + suffix + '.json' # set up keys that join inputs through various file forwardings: suffix = ana.galaxyFileId( galaxyInputFile) # suffix needs to be based on the input file if suffix == '-1': suffix = ana.fileGetPart(galaxyInputFile, 'root') inputKey = 'tags' + suffix + '.fastq' valDirKey = 'fastqValDir' + suffix valZipKey = 'fastqVal' + suffix + '.zip' valHtmlKey = 'fastqVal' + suffix + '.html' valJsonKey = 'fastqVal' + suffix + '.json' # Establish Inputs for galaxy and nonGalaxy alike ana.registerFile(inputKey, 'galaxyInput', galaxyInputFile) nonGalaxyInput = ana.nonGalaxyInput( inputKey) # Registers and returns the outside location # Output is complete dir ana.registerFile(valDirKey, 'galaxyOutput', galaxyOutputDir)
# Set up 'ana' so she can do all the work. If anaId matches another, then it's log is extended ana = GalaxyAnalysis(settingsFile, anaId, genome, expType) if testOnly: ana.dryRun = testOnly # What step expects: # # Inputs: 1 fastq file, pre-registered in the analysis keyed as: 'tags' + suffix + '.fastq' # Outputs: directory of files (will include html target) keyed as: 'fastqValDir' + suffix # zipped file of that directory keyed as: 'fastqVal' + suffix + '.zip' # html file in that directory keyed as: 'fastqVal' + suffix + '.html' # json file keyed as: 'fastqVal' + suffix + '.json' # set up keys that join inputs through various file forwardings: suffix = ana.galaxyFileId(galaxyInputFile) # suffix needs to be based on the input file if suffix == '-1': suffix = ana.fileGetPart(galaxyInputFile,'root') inputKey = 'tags' + suffix + '.fastq' valDirKey = 'fastqValDir' + suffix valZipKey = 'fastqVal' + suffix + '.zip' valHtmlKey = 'fastqVal' + suffix + '.html' valJsonKey = 'fastqVal' + suffix + '.json' # Establish Inputs for galaxy and nonGalaxy alike ana.registerFile(inputKey,'galaxyInput', galaxyInputFile) nonGalaxyInput = ana.nonGalaxyInput(inputKey) # Registers and returns the outside location # Output is complete dir ana.registerFile(valDirKey,'galaxyOutput',galaxyOutputDir) ana.createOutFile(valDirKey,'nonGalaxyOutput', '%s_sample_fastqc', ext='dir' )