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Limit concurrent fauna connections to 2 #202

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merged 2 commits into from
Jan 13, 2025
Merged

Limit concurrent fauna connections to 2 #202

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68ab301
Limit concurrent fauna connections to 2
joverlee521 Jan 10, 2025
123716a
Remove `message` directive from download_sequences
joverlee521 Jan 11, 2025
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11 changes: 10 additions & 1 deletion workflow/snakemake_rules/download_from_fauna.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,12 @@ titers = "data/{lineage}/{center}_{passage}_{assay}_titers.tsv"

'''

# Limit the number of concurrent fauna connections so that we are less likely
# to overwhelm the rethinkdb server.
# Inspired by the ncov's limit on concurrent deploy jobs
# <https://github.com/nextstrain/ncov/blob/20f5fc3c7032f4575a99745cee3238ecbeebb6e0/workflow/snakemake_rules/export_for_nextstrain.smk#L340-L362>
workflow.global_resources.setdefault("concurrent_fauna", 2)

# fields that will be canonicized by augur parse (upper/lower casing etc)

path_to_fauna = '../fauna'
Expand Down Expand Up @@ -42,11 +48,12 @@ def _get_virus_passage_category(wildcards):
return ""

rule download_sequences:
message: "Downloading sequences from fauna"
output:
sequences = "data/{lineage}/raw_{segment}.fasta"
params:
fasta_fields = config["fauna_fasta_fields"],
resources:
concurrent_fauna = 1
conda: "../envs/nextstrain.yaml"
benchmark:
"benchmarks/download_sequences_{lineage}_{segment}.txt"
Expand All @@ -71,6 +78,8 @@ rule download_titers:
dbs = _get_tdb_databases,
assays = _get_tdb_assays,
virus_passage_category=_get_virus_passage_category,
resources:
concurrent_fauna = 1
conda: "../envs/nextstrain.yaml"
benchmark:
"benchmarks/download_titers_{lineage}_{center}_{passage}_{assay}.txt"
Expand Down
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