def run_main(config,
config_file,
work_dir,
parallel,
fc_dir=None,
run_info_yaml=None):
"""Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
setup_logging(config)
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(
get_fastq_dir(fc_dir) if fc_dir else None, config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {
"fastq": fastq_dir,
"galaxy": galaxy_dir,
"work": work_dir,
"flowcell": fc_dir,
"config": config_dir
}
config = _set_resources(parallel, config)
run_parallel = parallel_runner(parallel, dirs, config, config_file)
# process each flowcell lane
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"],
fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("prep_recal", samples)
samples = recalibrate.parallel_write_recal_bam(samples, run_parallel)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("postprocess_variants", samples)
samples = combine_multiple_callers(samples)
samples = run_parallel("detect_sv", samples)
samples = run_parallel("combine_calls", samples)
run_parallel("process_sample", samples)
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
write_project_summary(samples)
write_metrics(run_info, fc_name, fc_date, dirs)
def run(self, config, config_file, run_parallel, dirs, lane_items):
lane_items = run_parallel("trim_lane", lane_items)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("prep_recal", samples)
samples = recalibrate.parallel_write_recal_bam(samples, run_parallel)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("postprocess_variants", samples)
samples = combine_multiple_callers(samples)
samples = ensemble.combine_calls_parallel(samples, run_parallel)
samples = run_parallel("detect_sv", samples)
samples = qcsummary.generate_parallel(samples, run_parallel)
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
return samples
def run(self, config, config_file, run_parallel, dirs, lane_items):
lane_items = run_parallel("trim_lane", lane_items)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("prep_recal", samples)
samples = recalibrate.parallel_write_recal_bam(samples, run_parallel)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("postprocess_variants", samples)
samples = combine_multiple_callers(samples)
samples = ensemble.combine_calls_parallel(samples, run_parallel)
samples = run_parallel("detect_sv", samples)
samples = qcsummary.generate_parallel(samples, run_parallel)
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
return samples
def run(self, config, config_file, run_parallel, parallel, dirs, lane_items):
raise NotImplementedError("`variant` processing is deprecated: please use `variant2`"
"The next version will alias variant to the new variant2 pipeline")
lane_items = run_parallel("trim_lane", lane_items)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("prep_recal", samples)
samples = recalibrate.parallel_write_recal_bam(samples, run_parallel)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("postprocess_variants", samples)
samples = combine_multiple_callers(samples)
samples = ensemble.combine_calls_parallel(samples, run_parallel)
samples = run_parallel("detect_sv", samples)
samples = qcsummary.generate_parallel(samples, run_parallel)
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
return samples
def run(self, config, config_file, run_parallel, parallel, dirs, lane_items):
raise NotImplementedError("`variant` processing is deprecated: please use `variant2`"
"The next version will alias variant to the new variant2 pipeline")
lane_items = run_parallel("trim_lane", lane_items)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("prep_recal", samples)
samples = recalibrate.parallel_write_recal_bam(samples, run_parallel)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("postprocess_variants", samples)
samples = combine_multiple_callers(samples)
samples = ensemble.combine_calls_parallel(samples, run_parallel)
samples = run_parallel("detect_sv", samples)
samples = qcsummary.generate_parallel(samples, run_parallel)
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
return samples
def run_main(config, config_file, work_dir, parallel,
fc_dir=None, run_info_yaml=None):
"""Run toplevel analysis, processing a set of input files.
config_file -- Main YAML configuration file with system parameters
fc_dir -- Directory of fastq files to process
run_info_yaml -- YAML configuration file specifying inputs to process
"""
setup_logging(config)
fc_name, fc_date, run_info = get_run_info(fc_dir, config, run_info_yaml)
fastq_dir, galaxy_dir, config_dir = _get_full_paths(get_fastq_dir(fc_dir) if fc_dir else None,
config, config_file)
config_file = os.path.join(config_dir, os.path.basename(config_file))
dirs = {"fastq": fastq_dir, "galaxy": galaxy_dir,
"work": work_dir, "flowcell": fc_dir, "config": config_dir}
config = _set_resources(parallel, config)
run_parallel = parallel_runner(parallel, dirs, config, config_file)
# process each flowcell lane
run_items = add_multiplex_across_lanes(run_info["details"], dirs["fastq"], fc_name)
lanes = ((info, fc_name, fc_date, dirs, config) for info in run_items)
lane_items = run_parallel("process_lane", lanes)
align_items = run_parallel("process_alignment", lane_items)
# process samples, potentially multiplexed across multiple lanes
samples = organize_samples(align_items, dirs, config_file)
samples = run_parallel("merge_sample", samples)
samples = run_parallel("prep_recal", samples)
samples = recalibrate.parallel_write_recal_bam(samples, run_parallel)
samples = parallel_realign_sample(samples, run_parallel)
samples = parallel_variantcall(samples, run_parallel)
samples = run_parallel("postprocess_variants", samples)
samples = combine_multiple_callers(samples)
samples = run_parallel("detect_sv", samples)
samples = run_parallel("combine_calls", samples)
run_parallel("process_sample", samples)
run_parallel("generate_bigwig", samples, {"programs": ["ucsc_bigwig"]})
write_project_summary(samples)
write_metrics(run_info, fc_name, fc_date, dirs)
