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Set threads for augur subsample #109

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Set threads for augur subsample #109

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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ Changes for this project _do not_ currently follow the [Semantic Versioning rule
Instead, changes appear below grouped by the date they were added to the workflow.

## 2026
* TBD: Optimized thread usage for `augur subsample`. [#109][]
* 25 February 2026: Changes to files referenced in `subsample` config will trigger a re-run of the rule. [#90][]
* 25 February 2026: Changes to non-subsampling config will no longer trigger a re-run starting from subsampling. [#91][]
* 09 February 2026: *MAJOR CHANGES* Switched ingest outputs to separate OPEN vs RESTRICTED files.
Expand Down Expand Up @@ -38,6 +39,7 @@ Instead, changes appear below grouped by the date they were added to the workflo
[#105]: https://github.com/nextstrain/measles/pull/105
[#107]: https://github.com/nextstrain/measles/pull/107
[#108]: https://github.com/nextstrain/measles/pull/108
[#109]: https://github.com/nextstrain/measles/pull/109
[530da56]: https://github.com/nextstrain/measles/commit/530da568d8014c08e73f31065a8fa96e5c2d2f20
[1cf1299...0313508]: https://github.com/nextstrain/measles/compare/1cf1299e1658140d9317fc9063f1e06ef04a6ee1...03135085aed310f1cb0d3ecb2dca342e6ec8f51d
[Pathoplexus]: https://pathoplexus.org
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4 changes: 3 additions & 1 deletion phylogenetic/rules/prepare_sequences.smk
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Expand Up @@ -3,7 +3,7 @@ This part of the workflow prepares sequences for constructing the phylogenetic t

See Augur's usage docs for these commands for more details.
"""
from augur.subsample import get_referenced_files
from augur.subsample import get_referenced_files, get_parallelism

rule subsample:
input:
Expand All @@ -15,13 +15,15 @@ rule subsample:
sequences = "results/genome/subsampled.fasta"
params:
strain_id = config["strain_id_field"]
threads: get_parallelism("results/genome/subsample_config.yaml", limit=workflow.cores)
shell:
"""
augur subsample \
--config {input.config} \
--sequences {input.sequences} \
--metadata {input.metadata} \
--metadata-id-columns {params.strain_id} \
--nthreads {threads} \
--output-sequences {output.sequences} \
"""

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4 changes: 3 additions & 1 deletion phylogenetic/rules/prepare_sequences_N450.smk
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Expand Up @@ -3,7 +3,7 @@ This part of the workflow prepares sequences for constructing the phylogenetic t

See Augur's usage docs for these commands for more details.
"""
from augur.subsample import get_referenced_files
from augur.subsample import get_referenced_files, get_parallelism

rule align_and_extract_N450:
input:
Expand Down Expand Up @@ -35,12 +35,14 @@ rule subsample_N450:
sequences = "results/N450/aligned.fasta"
params:
strain_id = config["strain_id_field"]
threads: get_parallelism("results/N450/subsample_config.yaml", limit=workflow.cores)
shell:
"""
augur subsample \
--config {input.config} \
--sequences {input.sequences} \
--metadata {input.metadata} \
--metadata-id-columns {params.strain_id} \
--nthreads {threads} \
--output-sequences {output.sequences} \
"""
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