v1.3.0

metavirs (v1.3.0)

Notable Changes

• a78a4af: Adding new dependency, XlsxWriter, to blast/v0.2.0 docker image.
• a78a4af: Adding improved script to create an excel spreadsheet from multiple input files.
• 7684769: Adding new rules to aggregate the blast-ed contigs from megahit and metaspades into two XLSX files.

Please run the metavirs cache sub-command to pull in the latest blast/v0.2.0 docker image.

v1.2.0

metavirs (v1.2.0)

Notable Changes

• 9a7ff3f: Adding script to download the latest nt viral database from NCBI's FTP site
• 2d45e22: Adding Dockerfile for latest version of ncbi-blast+.
• 99e99e5: Adding new rules to blast assembled contigs against the latest viral database.
• 7ba0c97: Creating additional resource bundle for the latest NCBI blast viral database and adding the bundle's chunks to the installer.

v1.1.0

metavirs (v1.1.0)

Notable Changes

• 551ea19: Adding onstart, onsuccess, and onerror hooks to get job information for submitted jobs
• 8963311: Adding jobby to parse and aggregate job details

v1.0.0

metavirs (v1.0.0)

Notable Changes

• 95369fa: Adding support for mixed single-end and paired-end inputs
• abad197: Adding dry-runs with paired-end, single-end, and mixed inputs
• a315652: Adding improved dark mode to docs
• f95851a: Adding Docker pulls and release information
• 26a9db1: Adding catch for github release edgecase
• 26a9db1: Passing memory limit to metaspades to avoid seg faults
• 7c8a2df: Moving default resources to OpenOmics shared group area
• 0198232: Adding script to create chunked resource bundles
• 6827d5e: Adding concurrent reference file downloader
• 351a737: Adding install sub command to download the pipeline's resource bundle
• 0765be5: Adding script to cache software containers locally
• 61318fa: Adding step to ensure tmp dir bind path resolves correctly
• f692c6c: Adding new option to provide path to a downloaded resource bundle
• e653b2a: Bumping up wall times of each assembler
• 09f11ff: Adding documentation new install sub command and other new features
• 9560a93: Reducing threads for better availibility of smaller clusters
• c34232b: Making prep_metaquast rule more fault tolerant

v0.2.0

Release v0.2.0

• Adding support for project-level aggregation, via the --aggregate flag
  • Creates an aggregated multi-sample interactive Krona report

v0.1.0-beta

metavirs (v0.1.0-beta)

Notable Changes

• d679a76: Adding basic scaffold for project
• e143480: New entry point to pipeline, ./metavirs
• ed2caa3: Convert bash script to snakemake rules
• acf7d30: Adding first draft of user documentation
• ed2caa3: Testing for functional equivalence
• b52ab45: Adding github actions workflow to build docs and dry run pipeline
• 5044819: Update output directory structure to match previous hierarchy

Roadmap

Future changes that are currently a work in progress and signify the authoring of a major milestone.

• Create docker image(s) with all run time dependencies
• Testing for functional equivalence (after adding docker images)
• Run pipeline on BigSky cluster

Contributors

@schaughencyp, @skchronicles