v2.4.1.0

What's Changed

New workflows or functionality

• add workflow "unpack_archive_to_bucket"; add task "unpack_archive_to_bucket_path" by @tomkinsc in #573
• assembly and genbank updates by @dpark01 in #579
• NCBI submission workflow updates, new workflow assemble_denovo_metagenomic, submit_biosample, submit_sra, submit_genbank. Prune vestigal workflows demux_metag, taxid_to_nextclade, contigs. by @dpark01 in #583

Workflow edits and fixes

• s/Array[File]+/Array[File?]+/g for tsv_files input in terra_tsv_to_table.wdl by @tomkinsc in #563
• bugfix: demux_deplete with biosample attributes by @dpark01 in #572
• scaffold_and_refine_multitaxa: add more output columns by @dpark01 in #574
• update workflows for genbank submission by @dpark01 in #576
• genbank bug fixes by @dpark01 in #581
• demux and nextclade updates by @dpark01 in #582
• genbank_single: made mapped bam input optional by @tomkinsc in #584
• Optimizations for Genbank submission of coinfections by @dpark01 in #587
• hotfix by @dpark01 in #590

New options, inputs, or outputs

• demux_deplete: allow multiple biosample attribute files by @tomkinsc in #561
• add contextual fasta input for augur_from_assemblies by @tomkinsc in #558
• add deduplication of sequences by ID in augur_from_assemblies by @tomkinsc in #564
• Expose --timetree parameter in refine_augur_tree by @lakras in #570
• Exposed --root-sequence parameter of augur ancestral by @lakras in #585
• report pct_top_hit_of_total_reads as one of the outputs of align_and_… by @tomkinsc in #577

Infrastructural updates

• update terra introspection to support GCP Batch backend by @tomkinsc in #575
• fix check_terra_env by @dpark01 in #589
• add task: download_from_url() to download a URL to a file by @tomkinsc in #562

Dependency changes

• update viral-core 2.3.6 -> 2.4.0 by @tomkinsc in #566
• bump viral core 2.4.0 -> 2.4.1 by @tomkinsc in #569
• bump pangolin and nextclade by @tomkinsc in #565
• bump viral-classify 2.2.4.2 -> 2.2.5 by @tomkinsc in #568
• remove exemption from global version pin for viral-core image used in check_terra_env; update viral-core spec of the task to 2.4.0 by @tomkinsc in #571

Build changes

• limit GH build concurrency by @tomkinsc in #549
• cleanup .dockstore.yml by @dpark01 in #578

Full Changelog: v2.3.6.0...v2.4.1.0