add busco tool #754
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add busco tool #754
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #754 +/- ##
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Coverage 46.08% 46.08%
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Files 78 78
Lines 7059 7059
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Hits 3253 3253
Misses 3806 3806 ☔ View full report in Codecov by Sentry. |
MrCreosote
reviewed
Aug 26, 2024
| @@ -62,10 +67,10 @@ | |||
| # if no specific metadata is provided for a tool, the default values are used. | |||
| TASK_META = {'gtdb_tk': {'chunk_size': 1000, 'exe_time': 65, 'tasks_per_node': 4, 'threads_per_tool_run': 32}, | |||
| 'eggnog': {'chunk_size': 100, 'exe_time': 15, 'node_time_limit': 0.5}, # Memory intensive tool - reserve more nodes with less node reservation time | |||
| 'busco': {'chunk_size': 50, 'exe_time': 90, 'node_time_limit': 1.5}, # 1.5 minutes per genome with a single task per node on the user's drive. TODO: Aim to test multi-threading per node along with scratch execution, and adjust `tasks_per_node` accordingly. | |||
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Wow this is expensive. For 10k genomes that's 250 hours, so scaling this to GTDB sized genome counts seems infeasible. Hopefully your TODOs pan out.
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