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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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Adding flu and RSV to TheiaCoV fastq workflows (VADR) #295

Closed kevinlibuit closed 3 months ago

kevinlibuit commented 6 months ago

:cool:

:pushpin: Explain the Request

Update the TheiaCoV fastq workflows (e.g. Illumina PE/SE, ONT, etc) to add VADR to influenza and RSV organism tracks, similar to TheiaCoV_FASTA

:books: Context

Will help laboratories perform QC of additional viral assemblies generated

:chart_with_upwards_trend: Desired Behavior

VADR outputs produced for more viral pathogens

kevinlibuit commented 6 months ago

Note: Flu will need to be added to all TheiaCoV workflows

cimendes commented 4 months ago

Flu and RSV models are available in the latest version of VADR (https://github.com/ncbi/vadr/wiki/Available-VADR-model-files) Docker container available from staph-b at us-docker.pkg.dev/general-theiagen/staphb/vadr:1.6.3

Commands to use:

FLU -r --atgonly --xnocomp --nomisc --alt_fail extrant5,extrant3 --mkey flu

RSV -r -xnocomp -mkey rsv

⚠️ WARNING: RSV Model uses over 30 GB of memory according to https://github.com/StaPH-B/docker-builds/blob/master/vadr/1.6.3/Dockerfile#L176-L177

We should be cautious when proceeding with RSV. Do we need to create two separate models for A and B to decrease the resource requirements?

cimendes commented 4 months ago

Solution: Pass the VADR memory requirement as input through the organism params sub-workflow