Comments (4)
The hardcoded defaults for v2 are here (branch v2):
nextclade/packages_rs/nextclade/src/align/params.rs
Lines 106 to 131 in 242d56f
For v3 (not stable, branch master) the hardcoded defaults are here:
nextclade/packages_rs/nextclade/src/align/params.rs
Lines 141 to 174 in 119cd4a
There are 2 important changes to consider in the upcoming Nextclade v3:
- alignment algo is changed quite a bit, so the params will change
- Nextalign executable is removed. Instead, Nextclade will take over the same job. In the new dataset format most files will be optional (and the dataset is also optional, so individual input args can be used) - all this to emulate the interface of Nextalign and to facilitate incremental development of datasets.
Because we are removing Nextalign, it does not make sense to add params into its help text anymore, as we are not planning any more releases.
Regarding Nextclade: the datasets can (and do) override parameters (using virus_properties.json
file for v2 and pathogen.json
in the v3), because different viruses sometimes need some different tuning. So I think that the displayed hardcoded number might be inaccurate and misleading, depending on which dataset you are planning to run. But let me know if you think it makes sense to add hardcoded defaults to Nextclade v3 anyways.
In the meantime, one thing you can try is to add -v
(--verbose
) flag to the run
command, and then the program should print the final values for this particular run, already taking into account values (in this order) in:
- dataset (if using Nextclade and if they are defined)
- CLI args (if an arg is provided)
- hardcoded defaults
UPD:
This statement is incorrect for v2:
already taking into account values (in this order) in
Nextclade/Nextalign v2 only print the CLI args, before merging-in the defaults, which is probably not very useful. This will change in v3.
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If you want to try Nextclade v3:
You can download prebuilt binaries on GitHub Actions:
- Filter runs by branch "master": https://github.com/nextstrain/nextclade/actions?query=branch%3Amaster
- Go to "Artifacts" section
- Click on artifact named "out". It will be downloaded as "out.zip", which contains binaries for all platforms
Or you can build it from source, from master branch, using our dev guide:
https://github.com/nextstrain/nextclade/blob/master/docs/dev/developer-guide.md
But v3 is not released and not stable yet. It's a bit of a crazy land still, and things might break. In which case you can try a slightly earlier version in the list of GitHub Actions. When things calm down a bit, we'll probably release an alpha version, or a few.
We appreciate early testing and feedback!
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Thanks @ivan-aksamentov! I will give both a try. I see v3 can be run without a dataset if --input-ref is provided, great. 🚀
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Related Issues (20)
- Custom datasets via URL param `dataset-url` HOT 4
- ENH: Show private aa substitutions in mutations tooltip HOT 1
- BUG(web/table): Empty strings make sort misbehave, not sort properly HOT 2
- Unaliased Pango Lineage column gone? HOT 14
- ENH(web): Allow us to hide a dataset from the dataset selector HOT 1
- Make Installation docs more prominent rather than GitHub releases?
- Possible CLI bug: TSV output not gzipped. HOT 3
- [v3] error attaching nodes to tree HOT 3
- Files required to configure a custom dataset when using nextclade for pathogens not provided by nextclade HOT 2
- Can Nextclade be used for HIV data? HOT 2
- why nextclade.csv download from the website can not in good format in excel? HOT 3
- Mutations relative to different references HOT 1
- Incorporation of enterovirus dataset into nextalde docker container HOT 1
- Include aligned sequences and translations in ndjson
- Maximum Sequence Limit? HOT 2
- Web: Grey scale coloring for region/country/divison if scale not predefined in reference tree HOT 5
- How to decide if the reversionSubstitutions are valid variants or not and whether to keep them? HOT 2
- Direct Auspice SVG Download
- ENH: enlarge Visualization when more nucleotides/Codons even if mutations not fall in striclty adjacent codons but close enough to need a whole view. HOT 2
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