def smartseq_flow3(sraInput, bt2Idx_ref, gtf_ref, fa_ref, threads):
fastq_dump = FastqDump(sraInput1=sraInput)
tophat = Tophat2(bt2Idx=bt2Idx_ref, gtfInput=gtf_ref)(fastq_dump)
sam2bam = SamToBam()(tophat)
bamsort = BamSort()(sam2bam)
cufflinks = Cufflinks(gtfInput=gtf_ref)(bamsort)
cuffmerge = Cuffmerge(faInput=fa_ref, gtfInput=gtf_ref)(cufflinks)
cuffquant = Cuffquant()(bamsort, cuffmerge)
cuffdiff = Cuffdiff(faInput=fa_ref)(cuffmerge, cuffquant)
Schedule.run()
def smartseq_flow2(sraInput, ht2Idx_ref, gtf_ref, fa_ref, threads):
fastq_dump = FastqDump(sraInput1=sraInput)
hisat = Hisat2(ht2Idx=ht2Idx_ref)(fastq_dump)
sam2bam = SamToBam()(hisat)
bamsort = BamSort()(sam2bam)
stringtie = Stringtie(gtfInput=gtf_ref)(bamsort)
cuffmerge = Cuffmerge(faInput=fa_ref, gtfInput=gtf_ref)(stringtie)
cuffquant = Cuffquant()(bamsort, cuffmerge)
cuffdiff = Cuffdiff(faInput=fa_ref)(cuffmerge, cuffquant)
Schedule.run()
from hcacn.steps import EasyTreat
from hcacn.core import Configure, Schedule
import os
#Configure.enableDocker(False)
Configure.setIdentity('cyliu')
pt = EasyTreat(
dgeInput='./step_13_DigitalExpression/out_gene_exon_tagged.dge.txt.gz')
Schedule.run()