metavirs - v1.4.0

metavirs (v1.4.0)

Notable Changes

• 19518eb: Updating docker image, removing un-used dependencies and adding taxonkit/0.18.0
• 35b3428: Adding contig length filter option to remove any annotated contigs less than its threshold (default: 500).
• 603d8c: Adding script to aggregate and summarize cov, counts, and annotations at different taxa levels, i.e family, genus, species.

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

Full Changelog: https://github.com/OpenOmics/metavirs/compare/v1.3.3...v1.4.0

- Python
Published by skchronicles over 1 year ago

metavirs - 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.

- Python
Published by skchronicles over 2 years ago

metavirs - 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.

- Python
Published by skchronicles almost 3 years ago

metavirs - 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

- Python
Published by skchronicles almost 3 years ago

metavirs - v1.0.0

metavirs (v1.0.0)

Notable Changes

• 95369fa60b0f18429fd073f523bf0d5832be3cd7: Adding support for mixed single-end and paired-end inputs
• abad1977655ae0813bfddc549d888a9576f87583: Adding dry-runs with paired-end, single-end, and mixed inputs
• a3156521ea6621bea457cc057f618f203e030a0c: Adding improved dark mode to docs
• f95851a9d8e7290460d295197e8b0798f9e1d465: Adding Docker pulls and release information
• 26a9db1fd35dc2cba8a0167493398c554738e80e: Adding catch for github release edgecase
• 26a9db1fd35dc2cba8a0167493398c554738e80e: Passing memory limit to metaspades to avoid seg faults
• 7c8a2dfda37fa0930987326c8a69864b6f64a8b2: Moving default resources to OpenOmics shared group area
• 019823219fe9b7b73f7ed54bdb170cd3874713d9: Adding script to create chunked resource bundles
• 6827d5e7f58ee36663d971b582711e06fce55835: Adding concurrent reference file downloader
• 351a737db201dc4505176975d5fcdecbe25390a6: Adding install sub command to download the pipeline's resource bundle
• 0765be56eb8523f851e45a944c53f4bc629252e1: Adding script to cache software containers locally
• 61318fa674b625267c2641f966f7b8b946beb5a2: Adding step to ensure tmp dir bind path resolves correctly
• f692c6c0fe8dc465af11ee3b6520b6acb08466d6: Adding new option to provide path to a downloaded resource bundle
• e653b2a9b8111acaa51306ce60efb38e367b37e3: Bumping up wall times of each assembler
• 09f11ffd24bf4beacf19a92d1c506ad37c3f2070: Adding documentation new install sub command and other new features
• 9560a93aab77a734332659201309308edf3ded54: Reducing threads for better availibility of smaller clusters
• c34232b649fe2642072cf194c627c486894ea715: Making prep_metaquast rule more fault tolerant

- Python
Published by skchronicles over 3 years ago

metavirs - 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

- Python
Published by skchronicles over 3 years ago

metavirs - v0.1.0-beta

metavirs (v0.1.0-beta)

Notable Changes

• d679a7616152effbd3a94dc7faa2769e0f02871e: Adding basic scaffold for project
• e143480a4c11226ad4ee7d00cf02d534b34bc05e: New entry point to pipeline, ./metavirs
• ed2caa3eb32d07c06ceb66090064693b66005540: Convert bash script to snakemake rules
• acf7d300c250a4d3de399f80e683d3eed4f0b830: Adding first draft of user documentation
• ed2caa3eb32d07c06ceb66090064693b66005540: Testing for functional equivalence
• b52ab454c71cca940485e2fe429bf60c8972a9f6: Adding github actions workflow to build docs and dry run pipeline
• 5044819ae8bab4fb342de97be62270f6e2404b52: 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

- Python
Published by skchronicles about 4 years ago