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KristinaGagalova / pante2-legacy

🍄 🧬An (improved) pipeline for predicting and masking transposable elements in multiple fungal genomes.
Apache License 2.0
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Optimize Infernal for cpus #25

Open KristinaGagalova opened 3 weeks ago

KristinaGagalova commented 3 weeks ago

The infernal step isn't properly using multiple cpus, it chunks the input into many parts, but then only processes them one at a time

JWDebler commented 3 weeks ago

I found the problem.

process runInfernal is labeled as a big_task, but has a hard coded --cpu 1 in the actual command.

replace --cpu 1 with --cpu "${task.cpus}" fixes that :-)