From 678c08f46dc786312b8770dc75894096e3f4bc41 Mon Sep 17 00:00:00 2001 From: j23414 Date: Wed, 29 Mar 2023 14:44:26 -0700 Subject: [PATCH] [wip] attempt at limiting concurrent deploys Since fetch_from_genbank can query NCBI up to 5 times for each of the serotypes, try to limit concurrent queries to under 3. Using 2 to be cautious. Following the format shown at: https://github.com/nextstrain/ncov/pull/1045 --- ingest/workflow/snakemake_rules/fetch_sequences.smk | 3 +++ 1 file changed, 3 insertions(+) diff --git a/ingest/workflow/snakemake_rules/fetch_sequences.smk b/ingest/workflow/snakemake_rules/fetch_sequences.smk index 7332b541..22c2d2c6 100644 --- a/ingest/workflow/snakemake_rules/fetch_sequences.smk +++ b/ingest/workflow/snakemake_rules/fetch_sequences.smk @@ -12,6 +12,7 @@ Produces final output as sequences_ndjson = "data/sequences_{serotype}.ndjson" """ +workflow.global_resources.setdefault("concurrent_deploys", 2) def download_serotype(wildcards): serotype = { @@ -24,6 +25,8 @@ def download_serotype(wildcards): return serotype[wildcards.serotype] rule fetch_from_genbank: + resources: + concurrent_deploys=1, output: genbank_ndjson="data/genbank_{serotype}.ndjson", params: