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@@ -168,6 +168,7 @@ def run(wf, config,
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parameters = {}
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+ # ====> 0-rawreads
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if general_config['input_type'] == 'raw':
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# Most common workflow: Start with rawreads.
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@@ -388,8 +389,9 @@ def run(wf, config,
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preads_fofn_fn = general_config['input_fofn']
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assert os.path.exists(preads_fofn_fn), '{!r} does not exist.'.format(preads_fofn_fn)
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- pdb_build_done = os.path.join(pread_dir, 'pdb_build_done')
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- run_jobs_fn = os.path.join(pread_dir, 'run_jobs.sh')
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+ # ====> 1-preads_ovl
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+ # pdb_build_done = os.path.join(pread_dir, 'pdb_build_done')
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+ # run_jobs_fn = os.path.join(pread_dir, 'run_jobs.sh')
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preads_db_fn = os.path.join(pread_dir, 'build', 'preads.db')
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length_cutoff_pr_fn = os.path.join(pread_dir, 'build', 'length_cutoff')
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@@ -443,6 +445,7 @@ def run(wf, config,
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dist=Dist(NPROC=4, job_dict=config['job.step.asm']),
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))
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+ # ====> 2-asm-falcon
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falcon_asm_done_fn = os.path.join(falcon_asm_dir, 'falcon_asm_done')
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for key in ('overlap_filtering_setting', 'length_cutoff_pr', 'fc_ovlp_to_graph_option'):
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parameters[key] = general_config[key]
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