broadinstitute/viral-ngs: v1.19.3

New:

• WDL workflow for Genbank submission [#797, #793, #800]
• metagenomics.py taxlevel_summary to tabulate taxonomic abundance data from multiple Kraken-format summary files. [#792]
• WDL workflow spikein to report spike-ins [#796]
• new contigs WDL workflow that runs depletion, SPAdes, and has a placeholder for future contig-based taxonomic classification steps to be added later [#796]
• sample name is now reported in Krona reports as the "root"-level name [#785]

Changed:

• WDL workflows for depletion now default to use an hg19 BWA database instead of an hg19 bmtagger database [#796]
• WDL assembly.scaffold: change name of final output file from {sample_name}.scaffold.fasta to {sample_name}.scaffolded_imputed.fasta [#796]

Fixed:

• Fixes and updates to tbl_transfer_prealigned --oob_clip behavior. [#807]
• Fixes version mismatch for tbl2asn spec [#787]
• Addresses edge cases of tbl2asn usage [#797]
• In Snakemake workflow, skip blank lines in samples-*.txt files [#794]
• bugfix ncbi annotation step in Snakemake workflow for Genbank submission prep [#786]

Added/Upgraded:

• dxWDL version 0.59->0.60.2 [#797]
• base image used for Docker container 0.1.8->0.1.9 to include security fixes from upstream [#802]