def fastrnaseqpipeline(config, run_info_yaml, parallel, dirs, samples):
samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)
with prun.start(_wres(parallel, ["samtools"]), samples, config,
dirs, "fastrnaseq") as run_parallel:
with profile.report("fastrnaseq", dirs):
samples = rnaseq.fast_rnaseq(samples, run_parallel)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for samples in samples:
run_parallel("upload_samples_project", [samples])
logger.info("Timing: finished")
return samples
def fastrnaseqpipeline(config, run_info_yaml, parallel, dirs, samples):
samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs,
samples)
with prun.start(_wres(parallel, ["samtools"]), samples, config, dirs,
"fastrnaseq") as run_parallel:
with profile.report("fastrnaseq", dirs):
samples = rnaseq.fast_rnaseq(samples, run_parallel)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for samples in samples:
run_parallel("upload_samples_project", [samples])
logger.info("Timing: finished")
return samples
def fastrnaseqpipeline(config, run_info_yaml, parallel, dirs, samples):
samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)
ww = initialize_watcher(samples)
with prun.start(_wres(parallel, ["samtools"]), samples, config,
dirs, "fastrnaseq") as run_parallel:
with profile.report("fastrnaseq", dirs):
samples = rnaseq.fast_rnaseq(samples, run_parallel)
ww.report("fastrnaseq", samples)
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
ww.report("qcsummary", samples)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for samples in samples:
run_parallel("upload_samples_project", [samples])
logger.info("Timing: finished")
return samples
def fastrnaseqpipeline(config, run_info_yaml, parallel, dirs, samples):
samples = rnaseq_prep_samples(config, run_info_yaml, parallel, dirs, samples)
ww = initialize_watcher(samples)
with prun.start(_wres(parallel, ["samtools"]), samples, config,
dirs, "fastrnaseq") as run_parallel:
with profile.report("fastrnaseq", dirs):
samples = rnaseq.fast_rnaseq(samples, run_parallel)
ww.report("fastrnaseq", samples)
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
ww.report("qcsummary", samples)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for samples in samples:
run_parallel("upload_samples_project", [samples])
logger.info("Timing: finished")
return samples
