def prep_qcprot(params):
conf = 'config.json'
if not os.path.isfile(conf):
db_temp = [os.path.basename(f) for f in params['db']]
dic = {'fasta': db_temp}
with open(conf, 'w') as fp:
json.dump(dic,fp)
wfdir = qproject.create(params['wfspace'],params['jobname'],params['wf'],params['inputfiles'],conf,params['user'],params['group'],params['db'])
print("copying inis to workflow directory")
#junk paths (-j). The archive's directory structure is not recreated; all files are deposited in the extraction directory (-d)
command = ['unzip','-j', params['params'], "-d", os.path.join(wfdir, "etc") ]
subprocess.check_call(command, shell=False)
return wfdir
def prep_rnaseq(params):
conf = 'config.json'
#here it is assumed that the portal prevents empty db
db_temp = params['db'][0]
db = db_temp.split(':')
if not os.path.isfile(conf):
dic = {'gtf': os.path.basename(db[1]), 'indexedGenome': os.path.basename(db[0]) + "/genome"}
with open(conf, 'w') as fp:
json.dump(dic, fp)
wfdir = qproject.create(params['wfspace'],params['jobname'],params['wf'],params['inputfiles'],conf,params['user'],params['group'])
#create link to database files
ref = os.path.join(wfdir,"ref")
ln(os.path.join(ref,os.path.basename(db[1])),db[1])
ln(os.path.join(ref,os.path.basename(db[0])),db[0])
return wfdir
def prep_maxquant(params):
conf = params['params']
wfdir = qproject.create(params['wfspace'],params['jobname'],params['wf'],params['inputfiles'],conf,params['user'],params['group'],params['ref'])
return wfdir