def chipseqpipeline(config, run_info_yaml, parallel, dirs, samples):
with prun.start(_wres(parallel, ["aligner", "picard"]),
samples, config, dirs, "multicore",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
with profile.report("organize samples", dirs):
samples = run_parallel("organize_samples", [[dirs, config, run_info_yaml,
[x[0]["description"] for x in samples]]])
with profile.report("alignment", dirs):
samples = run_parallel("prepare_sample", samples)
samples = run_parallel("trim_sample", samples)
samples = run_parallel("disambiguate_split", [samples])
samples = run_parallel("process_alignment", samples)
with profile.report("disambiguation", dirs):
samples = disambiguate.resolve(samples, run_parallel)
samples = run_parallel("clean_chipseq_alignment", samples)
with prun.start(_wres(parallel, ["peakcaller"]),
samples, config, dirs, "peakcalling",
multiplier = peaks._get_multiplier(samples)) as run_parallel:
with profile.report("peakcalling", dirs):
samples = peaks.peakcall_prepare(samples, run_parallel)
with prun.start(_wres(parallel, ["picard", "fastqc"]),
samples, config, dirs, "qc") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for sample in samples:
run_parallel("upload_samples_project", [sample])
logger.info("Timing: finished")
return samples
def chipseqpipeline(config, run_info_yaml, parallel, dirs, samples):
with prun.start(_wres(parallel, ["aligner", "picard"]),
samples, config, dirs, "multicore",
multiplier=alignprep.parallel_multiplier(samples)) as run_parallel:
with profile.report("organize samples", dirs):
samples = run_parallel("organize_samples", [[dirs, config, run_info_yaml,
[x[0]["description"] for x in samples]]])
with profile.report("alignment", dirs):
samples = run_parallel("prepare_sample", samples)
samples = run_parallel("trim_sample", samples)
samples = run_parallel("disambiguate_split", [samples])
samples = run_parallel("process_alignment", samples)
with profile.report("disambiguation", dirs):
samples = disambiguate.resolve(samples, run_parallel)
samples = run_parallel("clean_chipseq_alignment", samples)
with prun.start(_wres(parallel, ["peakcaller"]),
samples, config, dirs, "peakcalling",
multiplier = peaks._get_multiplier(samples)) as run_parallel:
with profile.report("peakcalling", dirs):
samples = peaks.peakcall_prepare(samples, run_parallel)
with prun.start(_wres(parallel, ["picard", "fastqc"]),
samples, config, dirs, "qc") as run_parallel:
with profile.report("quality control", dirs):
samples = qcsummary.generate_parallel(samples, run_parallel)
with profile.report("upload", dirs):
samples = run_parallel("upload_samples", samples)
for sample in samples:
run_parallel("upload_samples_project", [sample])
return samples
