adding "PacBio processing" to scripts #9
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antgonza
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antgonza
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lucaspatel
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Oct 28, 2025
| #SBATCH -n 1 | ||
| #SBATCH --time {{wall_time_limit}} | ||
| #SBATCH --mem {{mem_in_gb}}G | ||
| #SBATCH -o {{output}}/log-finish.out |
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Different log directory for this final job, is that intentional?
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It was, I think I'm gonna put it back where all the rest go in the next PR.
| main_fp, merge_fp = generate_minimap2_processing( | ||
| qclient, job_id, output_dir, parameters) | ||
| all_jids = [] | ||
| for step_id in range(1, total_steps + 1, 1): |
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Clever. Do we have a mechanism to handle resubmission if there's a failure in 1+ samples halfway through the steps?
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I think this will be very useful but not easy to integrate now. Only resubmit for that sample for the failed steps and all steps after it.
jianshu93
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Oct 28, 2025
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All slurm script look good.
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