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