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Release v2.1.0

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@github-actions github-actions released this 22 Nov 00:19
· 517 commits to main since this release
v2.1.0
c21e892

What's Changed

  • simplifying the container build to only use docker for now; the docker to apptainer conversion requires too much disk for github runners (c21e892)
  • simplifying container build ci to account for the fact that our monoimage is too big for standard github action runners (8989570)
  • trying another strategy for interop between docker and apptainer (945a33e)
  • giving the apptainer build proper permissions (1673a85)
  • switching to separate container image build checks for docker and apptainer (d6dd979)
  • correcting how github needs past docker builds to be cached (2850c59)
  • fixing pipeline validation CI, plus caching optimizations for the container image build CI (43f4e08)
  • fixing python script formatting and adding container build test CI that will produce a SIF image artifact for releases (11d8044)
  • naming (4f10b00)
  • guard list checking with sessionId or uuid ternary to allow users to set uuid (659f231)
  • adding more strict blast data upload handling (1be888d)
  • upload all the new columns (b7cd2af)
  • Add column naming for polars and removing header addition via echo command (86bb5e5)
  • make select blast rows work with the raw mega/blast results (2e109a0)
  • remove unused blast verification processes and python program (2a6fb31)
  • added new column to validation (63cc406)
  • adding more null and error handling to the lca finding utility function in the lca script (b9a3216)
  • removing faulty table of contents from readme for now (3f62d8a)
  • python formatting, a new cli wrapper, and updates to documentation in the readme and beyond (b229c84)
  • adding a new CI workflow to make sure the fancy new cli wrapper actually supports all params in nextflow.config (7e269cb)
  • adding a wrapper CLI to simplify usage, configuration, and setup (5e0e4ec)
  • adding an interactive install script with installation instructions in the docs (324133a)
  • updating example commands with new subworkflow name (1507890)
  • renaming the internal nvd2 workflow (c22b69f)
  • tidying up the newest python scripts with docstrings and bringing the LCA functionality properly into the pipeline (b4130b3)
  • adding a script that computes least common ancestors for the top blast hits for each contig (ca083db)
  • adjusting blastn to use the increased target count as well (bc8b336)
  • adding support for casting a wider net with blast and fixing two bugs in how blast results are handled/normalized before upload to labkey (e1996ec)

Contributors

Thanks to: Nicholas Minor,wkgardner

Version Information

  • Version: 2.1.0
  • Tag: v2.1.0
  • Commit: c21e892

Installation

Using this release with Nextflow:

nextflow run dhoconno/nvd -r v2.1.0 \
    --tools all \
    --samplesheet your_samples.csv \
    --experiment_id your_experiment_id \
    [other parameters...]

Development setup:

git clone --branch v2.1.0 https://github.com/dhoconno/nvd.git
cd nvd
pixi install --frozen
pixi shell

Documentation

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