ana.registerFile(valDirKey, 'galaxyOutput', galaxyOutputDir)
ana.createOutFile(valDirKey, 'nonGalaxyOutput', '%s_sample_fastqc', ext='dir')
ana.createOutFile(valZipKey, 'nonGalaxyOutput', '%s_sample_fastqc', ext='zip')
ana.createOutFile(valJsonKey, 'nonGalaxyOutput', '%s_validate', ext='json')
# Galaxy needs to know about a single file within the dir. While it is moved to the analysisDir
# as part of the htmlDir, It must be manually moved for galaxy. Thus, the standard
# analysis file forwarding is slightly modified here:
ana.registerFile(valHtmlKey, 'galaxyOutput', galaxyOutputHtml)
nonGalaxyOutput = ana.createOutFile(valHtmlKey,'nonGalaxyOutput', \
'%s_sample_fastqc/fastqc_report', ext='html' )
#ana.registerFile(valZipKey,'galaxyOutput',galaxyOutputZip) # No need: galaxy zips it anyway
jsonOut = ana.registerFile(valJsonKey, 'galaxyOutput', galaxyOutSummary)
# This step needs closer control of how files are delivered:
ana.deliveryKeys([valDirKey, valZipKey,
valJsonKey]) # Restrict file delivery to just these
ana.deliverToGalaxyKeys([valDirKey, valZipKey, valHtmlKey, valJsonKey
]) # Restrict delivery to these and in order
## TODO: methods for delivering json
# Establish step and run it:
step = FastqValidationStep(ana, suffix)
err = step.run()
# Determine success or failure by reading json output
# NOTE: if this test were in FastqValidationStep(), the results would not be delivered to galaxy!
if err == 0:
fp = open(jsonOut, 'r')
valJson = json.load(fp)
fp.close()
ana.registerFile(valDirKey,'galaxyOutput',galaxyOutputDir)
ana.createOutFile(valDirKey,'nonGalaxyOutput', '%s_sample_fastqc', ext='dir' )
ana.createOutFile(valZipKey,'nonGalaxyOutput', '%s_sample_fastqc', ext='zip' )
ana.createOutFile(valJsonKey,'nonGalaxyOutput','%s_validate', ext='json' )
# Galaxy needs to know about a single file within the dir. While it is moved to the analysisDir
# as part of the htmlDir, It must be manually moved for galaxy. Thus, the standard
# analysis file forwarding is slightly modified here:
ana.registerFile(valHtmlKey,'galaxyOutput',galaxyOutputHtml)
nonGalaxyOutput = ana.createOutFile(valHtmlKey,'nonGalaxyOutput', \
'%s_sample_fastqc/fastqc_report', ext='html' )
#ana.registerFile(valZipKey,'galaxyOutput',galaxyOutputZip) # No need: galaxy zips it anyway
jsonOut = ana.registerFile(valJsonKey,'galaxyOutput',galaxyOutSummary)
# This step needs closer control of how files are delivered:
ana.deliveryKeys([valDirKey,valZipKey,valJsonKey]) # Restrict file delivery to just these
ana.deliverToGalaxyKeys([valDirKey,valZipKey,valHtmlKey,valJsonKey]) # Restrict delivery to these and in order
## TODO: methods for delivering json
# Establish step and run it:
step = FastqValidationStep(ana,suffix)
err = step.run()
# Determine success or failure by reading json output
# NOTE: if this test were in FastqValidationStep(), the results would not be delivered to galaxy!
if err == 0:
fp = open(jsonOut, 'r')
valJson = json.load(fp)
fp.close()
grade = str(valJson['FastQC']['basic'])
