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