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KwanLab / Autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
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Add threads for for bowtie2-build #263

Open chasemc opened 2 years ago

chasemc commented 2 years ago

The number of cpus is already passed to the alignment step (see ${task.cpus}) so pass it to the build step as well

$ bowtie2-build --help | grep "threads"
  --threads <int>         # of threads

The commands are here:

https://github.com/KwanLab/Autometa/blob/b1ec370c44e7accfc917aaad1a685133537fd915/modules/local/align_reads.nf#L37