def quantitate_expression_parallel(samples, run_parallel): """ quantitate expression, all programs run here should be multithreaded to take advantage of the threaded run_parallel environment """ data = samples[0][0] samples = run_parallel("generate_transcript_counts", samples) samples = run_parallel("run_sailfish", samples) samples = sailfish.combine_sailfish(samples) if "cufflinks" in dd.get_expression_caller(data): samples = run_parallel("run_cufflinks", samples) #samples = run_parallel("run_stringtie_expression", samples) return samples
def quantitate_expression_parallel(samples, run_parallel): """ quantitate expression, all programs run here should be multithreaded to take advantage of the threaded run_parallel environment """ samples = run_parallel("generate_transcript_counts", samples) samples = run_parallel("run_cufflinks", samples) data = samples[0][0] if "sailfish" in dd.get_expression_caller(data): samples = run_parallel("run_sailfish", samples) samples = sailfish.combine_sailfish(samples) #samples = run_parallel("run_stringtie_expression", samples) return samples
def fast_rnaseq(samples, run_parallel): samples = run_parallel("run_salmon_index", [samples]) samples = run_parallel("run_salmon_reads", samples) samples = sailfish.combine_sailfish(samples) return samples
def fast_rnaseq(samples, run_parallel): # samples = run_parallel("run_rapmap_pseudoalign", samples) samples = run_parallel("run_salmon_reads", samples) samples = sailfish.combine_sailfish(samples) # samples = run_parallel("run_salmon_bam", samples) return samples
def fast_rnaseq(samples, run_parallel): samples = run_parallel("run_salmon_reads", samples) samples = sailfish.combine_sailfish(samples) return samples