v3.0.11.0

What's Changed

• bump viral-ngs to 3.0.9 by @dpark01 in #649
• bump viral-ngs 3.0.10, remove GATK IndelRealigner deps, update lofreq pipeline by @dpark01 in #650
• fix tar_extract: switch LOCAL to HDD disk, bump cpu and preemptible by @dpark01 in #651
• Bump docker image versions for ncbi-tools, nextclade, read-qc-tools, pangolin by @dpark01 in #652
• Adjust preemptible settings for assembly/metagenomics tasks by @dpark01 in #654
• Add rasusa-based coverage downsampling and tune preemptible settings by @dpark01 in #655

Full Changelog: v3.0.8.0...v3.0.11.0

v3.0.8.0

What's Changed

• bump py3-bio from 0.1.3 to 0.1.4 by @dpark01 in #646
• fix: update illumina import for viral-ngs 3.x namespace restructure by @dpark01 in #647
• bump viral-ngs and nextclade docker images by @dpark01 in #648

Full Changelog: v3.0.7.0...v3.0.8.0

v3.0.7.0

What's Changed

• bugfix: task terra.create_or_update_sample_tables by @dpark01 in #640
• Remove maxRetries to restore Cromwell call caching by @dpark01 in #641
• bump viral-ngs 3.0.6 to 3.0.7 by @dpark01 in #644
• move all viral-ngs WDL tasks back to quay.io from ghcr.io by @dpark01 in #645

Full Changelog: v3.0.6.0...v3.0.7.0

v3.0.6.0

What's Changed

• viral-ngs 3.0.5 to 3.0.6 by @dpark01 in #639

Full Changelog: v3.0.5.0...v3.0.6.0

v3.0.5.0

What's Changed

• viral-ngs: 3.0.5 by @dpark01 in #638

Full Changelog: v3.0.4.0...v3.0.5.0

v3.0.4.0

This release updates all viral-ngs docker dependencies to the refactored (but behaviorally the same) viral-ngs 3.x code repository (see more here). Among other things, all these images are now available ARM-native in addition to x86.

This release also makes some preparatory changes in anticipation of full WDL 1.1 support by Cromwell--this is mostly working out small differences between various executors (miniwdl, cromwell, dxCompiler) in their syntactical strictness in some edge cases. Full WDL 1.1 transition awaits some upstream bug fixes.

What's Changed

• Prepare WDL codebase for 1.1 upgrade by @dpark01 in #636
• Migrate to multiflavored viral-ngs:3.x docker images by @dpark01 in #637

Full Changelog: v2.5.21.1...v3.0.4.0

v2.5.21.1

What's Changed

• Add bbnorm preprocessing to align_reads for extremely large samples by @dpark01 in #630
• Add autoscaling memory for scaffold task based on reference genome size by @dpark01 in #631
• Bump viral-phylo to 2.5.21.5 - Fix DDBJ accessions and annotation transfer bugs by @dpark01 in #633
• bump py3-bio and viral-classify by @dpark01 in #634

Full Changelog: v2.5.21.0...v2.5.21.1

v2.5.21.0

What's Changed

• Add optional run_fastqc parameter to skip FastQC/MultiQC steps by @dpark01 in #618
• Add optional resource overrides to multiqc_from_bams and allowNestedInputs to bams_multiqc by @dpark01 in #619
• assemble_denovo_metagenomic optimization by @dpark01 in #620
• Add run_rmdup option and optimize single-bam handling in classification workflows by @dpark01 in #621
• Fix resource allocation issues in downsample and multiqc tasks by @dpark01 in #622
• bump viral-core 2.5.17 to 2.5.18 by @dpark01 in #623
• viral-assemble 2.5.16.0 to 2.5.18.0 by @dpark01 in #624
• fix SIGPIPE exit code 141 in scaffold task by @dpark01 in #625
• Improve rmdup_ubam memory handling for large samples by @dpark01 in #626
• Upgrade to viral-core 2.5.20 with optimized BAM filtering by @dpark01 in #627
• Integrate bbnorm normalization and optimize resource allocation by @dpark01 in #628
• Skip indel realignment for large BAMs in align_reads task by @dpark01 in #629

Full Changelog: v2.5.16.0...v2.5.21.0

v2.5.16.0

What's Changed

• Add pairwise_distances workflow and fix mafft_one_chr bug by @dpark01 in #610
• Fix unpack_archive_to_bucket_path to fail fast and optimize resources by @dpark01 in #611
• Dynamic resource allocation for demux, alignment, and depletion tasks by @dpark01 in #612
• Move FastQC execution from individual tasks into MultiQC task by @dpark01 in #614
• Add minimap2-based PAF streaming for spike-in counting and read depletion by @dpark01 in #615
• Restructure metadata flow and bump Docker images by @dpark01 in #616
• Add optional lane filter to find_illumina_files_in_directory task by @dpark01 in #617

Full Changelog: v2.5.10.0...v2.5.16.0

v2.5.10.0

What's Changed

• align_and_annot_transfer_single: parameterize mem; set default mem higher 15GB->30GB; increase cpu count 4->8; strip other fasta extensions in genbank_single and impose regex on assembly_id pattern; map 'sus scrofa [domesticus]' to 'swine' in biosample_to_genbank by @tomkinsc in #588
• run_discordance task: first index the ref fasta by @tomkinsc in #596
• genbank_single: add ability to custom override references by @dpark01 in #597
• bump viral-assemble to 2.4.2.0 by @dpark01 in #598
• bump vadr docker 1.6.3 to 1.6.4 model-free by @dpark01 in #599
• Add CLAUDE.md and bump viral-assemble to 2.4.3.1 by @dpark01 in #602
• Add simulate_illumina_reads workflow for synthetic test data generation by @dpark01 in #604
• bump viral-baseimage to 0.3.0; update version-wdl-runtimes.sh for cross-platform execution with either GNU/Linux or macOS/BSD syntax; set requirements-modules.txt path if unspecified by @tomkinsc in #601
• optimizations and more output for classify_single and assemble_denovo_metagenomic by @dpark01 in #605
• Fix MultiQC task failure when all input files are empty/invalid by @dpark01 in #606
• Fix MultiQC task to handle crashes from empty/invalid FastQC zip files by @dpark01 in #607
• Demultiplexing of Illumina flowcells optionally with inline barcodes by @tomkinsc in #600
• Implement load_illumina_fastqs workflow by @dpark01 in #609

Full Changelog: v2.4.1.1...v2.5.10.0