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WIP: Use metadata-only filtering in subsample jobs #571

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wants to merge 3 commits into from
Closed

WIP: Use metadata-only filtering in subsample jobs #571

wants to merge 3 commits into from

Commits on Apr 14, 2021

  1. Merge exclusion files on the fly in augur filter 

    Augur filter's new metadata-only interface will allow users to pass
multiple inputs to the `--exclude` argument, internally deduplicating
these strain lists. This new interface eliminates the need for a
separate Snakemake rule to cat the exclusion files.
    @huddlej
    huddlej committed Apr 14, 2021
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  2. Fix a typo in the masked file path on S3

    @huddlej
    huddlej committed Apr 14, 2021
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  3. Use metadata-only filtering for subsampling 

    Replaces FASTA outputs with strain list outputs for the subsample rule
such that sequence data are not inspected during most subsampling steps.
The exception to the rule are subsampling jobs that require a priority
score calculation that depends on the FASTA sequence of another
subsampled group. To handle this exception, we add a new rule to extract
just those subsampled sequences.

Finally, we collect subsampled sequences into a single deduplicated
FASTA output using augur filter's new interface with the `--exclude-all`
flag and multiple input support for `--include`.

Note that this commit also updates the conda environment to use a GitHub
branch instead of an official augur release.
    @huddlej
    huddlej committed Apr 14, 2021
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