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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
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[theiacov illumina wfs] Expose optional inputs for ivar consensus sub workflow #599

Open kapsakcj opened 2 months ago

kapsakcj commented 2 months ago

:cool:

:pushpin: Explain the Request

Internal request (from me) that came up because a user was analyzing illumina PE data with very large FASTQs and caused the ivar consensus task to run out of memory. Apparently the default 16GB was not enough.

Would be good to expose optional inputs for cpu, ram, docker, etc. for all steps in the ivar consensus subworkflow: https://github.com/theiagen/public_health_bioinformatics/blob/main/workflows/utilities/wf_ivar_consensus.wdl

kapsakcj commented 2 months ago

the specific task in the subworkflow that failed was the consensus task and it would be good for the user have the ability to increase the memory manually, as the memory retry feature did not work since the killed error occurred early in the one-liner containing pipes.

See issue #598 for more details