# 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' )
