def __init__(
self,
root_ctg,
ctgfasta_path,
reads_ctg_bam_path,
input_fqs,
asmrootdir_path,
# FIXME hack to get stdout logged
logger,
):
self.root_ctg = root_ctg
self.ctgfasta_path = ctgfasta_path
self.reads_ctg_bam_path = reads_ctg_bam_path
self.asmrootdir_path = asmrootdir_path
self.logger = logger
self.tenxfq_paths = list(glob.glob(input_fqs))
self.fqdir_path = os.path.join(self.asmrootdir_path, 'fqs')
util.mkdir_p(self.asmrootdir_path)
util.mkdir_p(self.fqdir_path)
self.debugdir_path = os.path.join(self.asmrootdir_path, 'debug')
util.mkdir_p(self.debugdir_path)
self.ctg_size_map = util.get_fasta_sizes(self.ctgfasta_path)
def run(options):
"""
1. create output directories
2. collect args for each stage
3. check which stages need to run
4. iterate through stages and submit jobs
5. validate that we're done running
"""
util.mkdir_p(options.output_dir)
util.mkdir_p(options.results_dir)
util.mkdir_p(options.working_dir)
util.mkdir_p(options.log_dir)
stages = get_stages(options)
runner = pipeline.Runner(options)
for stage_name, stage in stages.items():
runner.run_stage(stage, stage_name)