Release v2.3.6.0 · broadinstitute/viral-pipelines

What's Changed

update enterics visualization docker image by @jpramosbarroso in #516
Make create_enterics_qc_viz whitespace tolerant by @dpark01 in #517
update personal branch by @jpramosbarroso in #520
create_enterics_qc_viz simplify and improve portability by @jpramosbarroso in #521
update docker for try/except block with new error message by @jpramosbarroso in #522

scaffold_and_refine_multitaxa -- more thorough assembly outputs by @dpark01 in #524
scaffolding and reference selection based on ANI by @dpark01 in #528
Reference selection improvements and nextclade generalization by @dpark01 in #529
scaffolding regression fixes plus docker updates by @dpark01 in #547
scaffold multitaxa: drop empty assembly output rows by @dpark01 in #554
report reference genome length in align_reads output; use this value for assemble_refbased. reference_genome_length by @tomkinsc in #538

demux_deplete: make depletion optional, load biosample metadata to tables by @dpark01 in #551
demux_deplete small updates by @dpark01 in #552
demux_deplete fixes/updates by @dpark01 in #555

allow additional options for picard in FastqToUBAM by @tomkinsc in #518
WDL code/style cleanups by @dpark01 in #523
expanded parameterization of align_and_count and additional output metrics by @tomkinsc in #525
guard against shell pipefails in align_and_count in instances where empty inputs would result in div-by-zero conditions by @tomkinsc in #535
classify_single: parameterize taxa to deplete by @dpark01 in #536
bugfix fetch_sra_to_bam by @tomkinsc in #542
Update polyphonia input parameters and defaults by @lakras in #545

build and container updates by @dpark01 in #526
update viral-core 2.3.0 -> 2.3.1 by @tomkinsc in #527
increase default instance memory for kraken2 task 72 -> 90GB by @tomkinsc in #540
nextclade updates by @dpark01 in #557
bump upstream docker images by @dpark01 in #556

Full Changelog: v2.2.4.0...v2.3.6.0