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biocore / oecophylla

shotgun pipeline
MIT License
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Comet #127

Closed tanaes closed 6 years ago

tanaes commented 6 years ago

@qiyunzhu

tanaes commented 6 years ago

note that the localscratch on Comet has to be specified as so:


oecophylla workflow \
--test \
--cluster-config cluster_configs/comet/cluster.json \
--local-scratch '/scratch/$USER/$SLURM_JOB_ID' \
--workflow-type profile \
--profile cluster_configs/comet \
--output-dir test_out \
-j 16 \
all

i am thinking about ways that this could be integrated into the cluster config.yaml file

qiyunzhu commented 6 years ago

Looks good! Thanks for solving this critical problem!