broadinstitute/viral-ngs: v1.19.1

New:

• [#762] The taxon_filter.py file now has a new command, deplete_bwa_bam, which uses bwa for depletion of sequence data provided in *.fasta format or pre-indexed bwa database format.
• [#762] bwa-based depletion is now available as an option in taxon_filter.py deplete via the --bwaDbs argument

Changed:

• The taxon_filter.py deplete_human command is now deprecated in favor of taxon_filter.py deplete. The deplete_human command will remain for the time being for compatibility.
• [#755, #766] Add a new align_and_plot workflow in WDL, Cromwell, DNAnexus.

Fixed:

• [#761] Fix a tar extraction bug when running within the Docker container as root
• [#765] Fix TruSight illumina indexes
• [#760] Prevent ambiguous contig alignment during scaffolding from causing hard failures (warn and proceed with remaining contigs)
• [#741] When scaffolding against multiple reference genomes, allow some to fail, as long as some succeed

Added/Upgraded:

• [#752, #750, ] DNAnexus workflows now include defaulted file parameters for various databases
• [#751] MVicuna duplicate removal is now parallelized if multiple read groups exist in the input BAM
• [#756, #767] Docker viral-baseimage upgraded from 0.1.6 (zesty) to 0.1.8 (artful) with fixes for Spectre and Meltdown

Documentation:

• [#768] fixed explanation of manual conda installation
• [#739] removed deprecated virtualized install from docs
• [#746] explain flowcells.txt a bit more