WFL-compatible one-shot workflow #356
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This PR prepares
sarscov2_illumina_fullfor use by workflow launcher in Terra off the Terra Data Repo. The main requirement is that the bulk of the compute happens in a single automated all-in-one workflow that is launchable with strictly the data coming from the data repo plus any invariant workspace variables. This PR accomplishes this by incorporatingsarscov2_biosample_loadas a subworkflow at the beginning ofsarscov2_illumina_full. This invocation is optional and only happens if the requiredArray[File] biosample_attributesvariable is an empty list. If this is empty, we interpret this to mean that BioSamples have not been registered and that the attributes table needs to be generated by calling sarscov2_biosample_load. The rest of the normal workflow proceeds as usual.After merging this PR, WFL will be able to automate the vast majority of compute after sequencing is complete, from BioSample registration, to demux, depletion, assembly, lineage calling, and preparation of all submission (genbank, sra, gisaid) packages. Users would then need to subsequently follow this run with
sarscov2_sequencing_reportsto generate a cumulative metadata tsv, and thensarscov2_data_releaseif all looks good (the cumulative metadata tsv is required for delivery to CDC OAMD, but not NCBI or GISAID).