Releases: OpenOmics/nanite
v0.6.0
nanite (v0.6.0)
New feature: assemble and recover viral genomes.
Added a new feature called, --assemble-reads, to assemble and recover high-quality viral genomes.
- Updated the docker image and conda environment for new required dependencies: flye and viralFlye.
- To use the latest version of the pipeline, please re-build or create a new conda environment using the provided conda environment file. If you are using singularity, please pull the latest docker image using the using the cache sub command.
- Added new rules to assemble and recover high-quality viral genomes with flye and viralFlye, the recovered viralFlye genomes are aligned against our NCBI viral database and the results are visualized with krona.
- The interactive krona report can be found in the following location in the output directory:
{sample}/assembly/reports/{sample}_viralflye_classification.html.
- The interactive krona report can be found in the following location in the output directory:
Full Changelog: v0.5.1...v0.6.0
v0.5.0
nanite (v0.5.0)
Adding a new --conda-env-name option to the run command to use conda/mamba in an offline mode.
Notable changes:
Previously, the --use-conda option would build a conda environment on the fly when the pipeline was invoked. The new option called --conda-env-name allows a user to point to an existing, name conda environment. This is beneficial because building a new conda/mamba environment can be slow. Also, the build process requires access to the internet. With that being said, for some users it may make sense for them to build the conda environment once and reuse it. This will skip rebuilding the conda environment over and over again, and it will ensure the pipeline can run in an offline mode with conda.
Please see our TLDR for running conda in an offline mode on the setup page.