streamline NCBI submissions #191
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…d in workflow yet)
…nbanks source modifier table
…post metadata merge in subsample_by_metadata_with_focal
…evel options properly
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adds sarscov2_genbank workflow, which preps assemblies for submission to genbank using their new process for SARS-CoV-2 (use the previous workflows for other taxa--though my guess is that genbank will roll these changes out across taxa eventually)
adds the VADR (Viral Annotation DefineR) tool, written by genbank, to produce tbl files on assemblies and pre-screen submissions to those that are expected to pass QC on NCBI's end
adds sra_meta_prep task and the new demux_deplete workflow, which runs demux on all lanes of a flowcell, runs human read depletion, and packages cleaned reads for SRA submission (requires a more verbose custom samplesheet than the default Illumina sheets and requires pre-registered NCBI BioSamples, but this should be used for all high throughput sequencing projects)
some preliminary work on an end-to-end SARS-CoV-2 pipeline (sarscov2_illumina_full), but it is not quite ready yet
bump pangolin and nextclade docker images
incorporate metadata tsv merging to augur_from_msa
replace augur_from_assemblies to incorporate tsv merging, derivedcols, subsample_by_metadata_with_focal and augur_from_msa, turning it into an end-to-end pipeline from global database download, merged in with custom data, to new nextstrain builds (takes a while though)