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Update subsample inputs - #90

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victorlin/augur-subsample-resolves-filepaths
Feb 25, 2026
Merged

Update subsample inputs#90
victorlin merged 5 commits into
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victorlin/augur-subsample-resolves-filepaths

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@victorlin victorlin commented Oct 24, 2025 •
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Description of proposed changes

This PR applies fixes for nextstrain/public#31 to this repo.

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  • Tested locally

    Command 
    $ nextstrain run . phylogenetic tmp
…
Validating schema of 'results/genome/subsample_config.yaml'...
Select jobs to execute...
[early] Sampling at 2000 per group.
[early] 25669 strains were dropped during filtering
[early]         3 were dropped because they were in /nextstrain/pathogen/phylogenetic/defaults/dropped_strains.txt
[early]         4 were dropped because they were earlier than 1950.0 or missing a date
[early]         2955 were dropped because they were later than 2021.09 or missing a date
[early]         22557 were dropped because they were shorter than the minimum length of 5000bp when only counting standard nucleotide characters A, C, G, or T (case-insensitive)
[early]         150 were dropped during grouping due to ambiguous year information
[early]         6 were added back because they were in /nextstrain/pathogen/phylogenetic/defaults/include_strains_genome.txt
[early]         6 were dropped because of subsampling criteria
[early] 961 strains passed all filters
[late] Sampling at 2000 per group.
[late] 25911 strains were dropped during filtering
[late]  3 were dropped because they were in /nextstrain/pathogen/phylogenetic/defaults/dropped_strains.txt
[late]  17634 were dropped because they were earlier than 2021.09 or missing a date
[late]  8130 were dropped because they were shorter than the minimum length of 5000bp when only counting standard nucleotide characters A, C, G, or T (case-insensitive)
[late]  150 were dropped during grouping due to ambiguous year information
[late]  6 were added back because they were in /nextstrain/pathogen/phylogenetic/defaults/include_strains_genome.txt
[late]  0 were dropped because of subsampling criteria
[late] 719 strains passed all filters
24957 strains were dropped during filtering
        26630 were dropped by `--exclude-all`
        961 were added back because they were in /tmp/sample_early_yf20o07i
        719 were added back because they were in /tmp/sample_late_uiwmbobm
1673 strains passed all filters

  • Checks pass

  • Update changelog

  • Merge config: Set AUGUR_SEARCH_PATHS shared#68 and git subrepo pull

  • Pre-merge: update changelog to replace TBD

@victorlin victorlin self-assigned this Oct 24, 2025
This was referenced Oct 24, 2025
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victorlin force-pushed the victorlin/custom-config-merge branch from 3980377 to e78aadc Compare October 29, 2025 22:17
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victorlin force-pushed the victorlin/augur-subsample-resolves-filepaths branch from e751070 to 8c07397 Compare October 29, 2025 22:17
@victorlin
victorlin force-pushed the victorlin/augur-subsample-resolves-filepaths branch from 8c07397 to 2e547d7 Compare January 27, 2026 19:58
@victorlin
victorlin changed the base branch from victorlin/custom-config-merge to main January 27, 2026 19:58
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victorlin force-pushed the victorlin/augur-subsample-resolves-filepaths branch from 2e547d7 to e3a2110 Compare January 27, 2026 20:08
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joverlee521
joverlee521 reviewed Jan 27, 2026
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Comment thread phylogenetic/rules/config.smk
jameshadfield
jameshadfield reviewed Jan 28, 2026
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Comment thread phylogenetic/rules/prepare_sequences.smk
jameshadfield
jameshadfield reviewed Jan 28, 2026
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Comment thread phylogenetic/Snakefile Outdated
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victorlin force-pushed the victorlin/augur-subsample-resolves-filepaths branch from e3a2110 to de3e323 Compare January 29, 2026 23:58
victorlin
victorlin commented Jan 30, 2026
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Comment thread shared/vendored/snakemake/config.smk
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@victorlin
victorlin force-pushed the victorlin/augur-subsample-resolves-filepaths branch from de3e323 to a062d7d Compare February 4, 2026 18:45
@victorlin victorlin changed the title Resolve filepaths within augur subsample and add them as rule input Update subsample inputs Feb 4, 2026
@victorlin

victorlin commented Feb 4, 2026

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Changes from #91 are now part of this PR – see #91 (comment)

@victorlin
victorlin force-pushed the victorlin/augur-subsample-resolves-filepaths branch from a062d7d to 875afc4 Compare February 4, 2026 21:22
@victorlin victorlin mentioned this pull request Feb 4, 2026
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victorlin and others added 2 commits February 10, 2026 14:54
@victorlin
git subrepo pull (merge) shared/vendored
3553061 
subrepo:
  subdir:   "shared/vendored"
  merged:   "37cf39c"
upstream:
  origin:   "https://github.com/nextstrain/shared"
  branch:   "main"
  commit:   "37cf39c"
git-subrepo:
  version:  "0.4.9"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "4f60dd7"
@victorlin
Validate build names
af3d4b3 
This prevents invalid build names from being evaluated for output.

Changes the error from:

    MissingInputException in rule all in file "/nextstrain/build/phylogenetic/Snakefile", line 26:
    Missing input files for rule all:
        affected files:
            auspice/measles_foo_tip-frequencies.json
            auspice/measles_foo.json

to:

    ERROR: The following names in 'builds' are not valid:

        foo

    Valid builds are:

        genome
        N450

Copied from wnv repo with some small adjustments.¹

¹ https://github.com/nextstrain/WNV/blob/009e0183863ccb532de2882af814d0c15a53dc64/phylogenetic/rules/config.smk#L1
@victorlin
victorlin force-pushed the victorlin/augur-subsample-resolves-filepaths branch from 875afc4 to 49bce21 Compare February 10, 2026 22:54
@victorlin victorlin mentioned this pull request Feb 21, 2026
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victorlin and others added 3 commits February 25, 2026 10:58
@victorlin
Write job-specific subsampling config files
be988eb 
This prevents unrelated config changes from triggering a re-run of augur
subsample.
@victorlin
Resolve filepaths within augur subsample
b6f4dd8 
… instead of doing this in the workflow upfront.

Requires Augur version 32.1.0 or later.
@victorlin
Add resolved filepaths as rule input
de0c723 
This takes advantage of the Snakemake feature that detects input file
changes to re-run jobs.
@victorlin
victorlin force-pushed the victorlin/augur-subsample-resolves-filepaths branch from 49bce21 to de0c723 Compare February 25, 2026 18:58
@victorlin
victorlin merged commit 48b10b1 into main Feb 25, 2026
5 checks passed
@victorlin
victorlin deleted the victorlin/augur-subsample-resolves-filepaths branch February 25, 2026 19:01
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