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Release v2.0.0

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@github-actions github-actions released this 28 Aug 15:06
· 576 commits to main since this release
v2.0.0
c7cf9dc

Overview

Time to release NVD version 2.0, henceforth to be referred to a NVD2🥳

NVD2 is a ground-up rewrite of the entirety of NVD1, a Snakemake workflow, in the Nextflow language. It also ships with fully containerized dependencies, including a working image on Docker Hub, new and improved, publicly available reference databases, a new Pixi-based conda project management system, enhanced cloud-deployment capabilities, vastly improved, fine-grained configurability, expanded documentation, integrations for data display on LabKey laboratory data management systems, and more. In addition to complete feature parity with NVD1, NVD2 adds new features, including GOTTCHA2 for expanded metagenomic classification beyond human viruses, as well as human read scrubbing and sequencing data compression optimization using clumpify.

More details on all the changes that transformed v1.0 to v2.0 are below. We encourage any users or contributors to open issues about any bugs or feature requests. At the time of this release, NVD2 is actively maintained and in use by the O'Connor Group at University of Wisconsin - Madison.

What's Changed

  • adding more license information to the readme in prep for a release (c7cf9dc)
  • removed unused param (7d12f85)
  • optional read scrubbing (79cc075)
  • fixing the gating of clumpify behind successful completions of the other subworkflows (c15843d)
  • finishing touches to the new readme (6852e91)
  • restoring copyleft license we're now stuck with (639d774)
  • adding many more docs and a filled out readme (5fc059d)
  • added optional human read scrubbing (35d6f57)
  • added human read filtering for SRA publishing. (90a5308)
  • tool handling and removing redundant params (017e9aa)
  • fix gottcha2 db wildcard channel input declaration error (a7f2fc0)
  • pushing a rudimentary readme for NVD2 (a81b593)
  • added nvd webdav upload (ab2b46c)
  • gottcha2 file bundling with webdav working (331e0d1)
  • webdav upload working (163be40)
  • getting rid of deprecated blast verification outputs for gottcha2 (65dbfe6)
  • labkey option boolean (908f5b0)
  • parameterizing the minimum number of reads needed for gottcha2 to a relatively conservative level (792287f)
  • producing the lineage tsv from the fasta extraction step in gottcha2 with the name expected downstream (2fa0349)
  • fixing tuple cardinality for the gottcha2 compression passthrough process (a366a4e)
  • Merge branch 'nvd-2.0-pre-alpha' of https://github.com/dhoconno/nvd into nvd-2.0-pre-alpha (528fbf2)
  • filtering to only FASTQs that have at least 100 reads (note: this is hardcoded currently!) for gottcha2 (3fb7cd8)
  • filtering to only FASTQs that have at least 100 reads (note: this is hardcoded currently!) for gottcha2 (7c763f4)
  • putting gottcha2 into verbose debug mode for debugging (06b59b8)
  • making gottcha2 generate fasta output optional (28e7b88)
  • fixing gottcha2 publish directory param calls (5b95856)
  • turning results publishing back on for gottcha2 (ce6f8b2)
  • rejiggering lockfile (ca67389)
  • Merge branch 'nvd-2.0-pre-alpha' of https://github.com/dhoconno/nvd into nvd-2.0-pre-alpha (29af65b)
  • working containerfile and nextflow config updates to pull it in from docker hub (a152e12)
  • working containerfile and nextflow config updates to pull it in from docker hub (69d4bc8)
  • Remove hard coding and instead pass them as command line args (0ea0c3a)
  • Labkey uploading by default is now false (0179678)
  • NVD2 packages added (382742a)
  • added whitelisted strain specific blasting (3b2e423)
  • swap fasta upload to after multimaps are removed (e80e25f)
  • Added downsampling to strain and species for last verification (d0c5e96)
  • layering additional updates including integration of gottcha2 blast verification (67f156c)
  • LabKey intergration working for both Gottcha2 and nvd2 (c668764)
  • added experiment id uniqueness for lists (3efcd2e)
  • nvd2 LK validation check (392ca9b)
  • Utilize nextflow secrets (69917e4)
  • Remove large python code from script blocks in process definitions for LabKey uploads (702bf9d)
  • adding error strategies to more processes and assigning publish directories in a results directory with an intuitive hierarchy (7f70aab)
  • revert (7632889)
  • bad yank paste (a21c688)
  • LabKey upload of blast results working with nvd2 (e925dd0)
  • LabKey upload for STAT human viruses beta added and working with test data. (896067d)
  • handling the fact that gottcha2 does not support compressed inputs (35d6128)
  • final touches on clumpify implementation (4543e16)
  • adding a clumpify subworkflow (c11488f)
  • fixing param calls in main (9f10838)
  • plugging in gottcha2 (dc8bbfe)
  • Merge branch 'nvd-2.0-pre-alpha' of https://github.com/dhoconno/nvd into nvd-2.0-pre-alpha (bc0f255)
  • Complete overhaul of the initial NVD2.0 prototype to get a run to completion with our small Sapovirus test dataset (8acf95c)
  • fixing an unclosed bracket in nextflow.config (daa0c77)
  • fleshing more of the data input steps (272e8c2)
  • and he said 'let there be nextflow' (85f9cd0)
  • Update config.yaml (0aeeda4)
  • Update README.md (fec3949)
  • Update Snakefile (daaac63)
  • Merge pull request #2 from pathogenuity/main (2047365)
  • merge to add better logging (c9143cd)
  • update logging of shell invokations (69f6040)
  • Add files via upload (e97fe70)
  • Delete nvd_flow.png (1faaa80)
  • Update README.md (2001f5d)
  • merge (8266969)
  • Merge branch 'main' of https://github.com/dhoconno/nvd (326746a)
  • update gitignore (c4c4c1f)
  • Update README.md (616acd0)
  • Update README.md (e54f006)
  • Add files via upload (a734736)
  • Delete nvd_flow.png (f4dee86)
  • update NVD workflow with ARGOS (3398036)
  • Merge pull request #1 from dhoconno/30844 (ff54ce2)
  • update config (97885d9)
  • change threshold for hq argos to 2000bp (f2a4fc7)
  • with demo data for Github (f0de42c)
  • working nvd with argos - deploy to CHTC (8a7a72b)
  • add argos labkey upload (fbfb534)
  • refactor to use labkey (a8f27b8)
  • run WNPRC samples (df8b6b1)
  • aggregation working (6005795)
  • working aggregation (68d778f)
  • making extracted BAM and FASTA for inspection (1a060f5)
  • add genome coverage (7920e42)
  • working to bait sequences that could be perfect matches to reduce exhaustive searching computation (63d22cf)
  • create concatenated argos file for baiting (682c703)
  • avoid collisions by using bbmap nodisk for indices (0550b08)
  • incorporate revisions made on MEL-SFO flight (2e69426)

Contributors

Thanks to: David O'Connor,Nicholas Minor,William-Gardner-Biotech,dho,dhogal2,will,wkgardner

Version Information

  • Version: 2.0.0
  • Tag: v2.0.0
  • Commit: c7cf9dc

Installation

Using this release with Nextflow:

nextflow run dhoconno/nvd -r v2.0.0 \
    --tools all \
    --samplesheet your_samples.csv \
    --experiment_id your_experiment_id \
    [other parameters...]

Development setup:

git clone --branch v2.0.0 https://github.com/dhoconno/nvd.git
cd nvd
pixi install --frozen
pixi shell

Documentation

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