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Enable multithreading to avoid 6hr time-out during github action #45

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merged 1 commit into from
Nov 20, 2024
Merged

Enable multithreading to avoid 6hr time-out during github action #45

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3 changes: 3 additions & 0 deletions ingest/profiles/default/config.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
cores: all
printshellcmds: true
Comment on lines +1 to +2
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not asking for a change

In case it's not clear, these configs are not necessary when running the builds with the Nextstrain CLI via nextstrain build.

  1. CLI will use all cores if the --cpus option is not provided (ref).
  2. The --printshellcmds flag is passed to snakemake by default (ref)

rerun-incomplete: true
2 changes: 2 additions & 0 deletions ingest/rules/nextclade.smk
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Expand Up @@ -65,11 +65,13 @@ rule nextclade_classify:
dataset=config["nextclade"]["nextclade_dataset_path"],
output:
nextclade_tsv="data/nextclade_results/nextclade.tsv",
threads: workflow.cores,
shell:
"""
nextclade3 run \
--input-dataset {input.dataset} \
--output-tsv {output.nextclade_tsv} \
--jobs {threads:q} \
--silent \
{input.sequences}
"""
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3 changes: 3 additions & 0 deletions phylogenetic/profiles/default/config.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
cores: all
printshellcmds: true
rerun-incomplete: true
5 changes: 2 additions & 3 deletions phylogenetic/rules/construct_phylogeny.smk
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Expand Up @@ -29,15 +29,14 @@ rule tree:
"logs/tree.txt",
benchmark:
"benchmarks/tree.txt"
params:
threads = workflow.cores,
threads: workflow.cores
shell:
"""
augur tree \
--alignment {input.alignment} \
--output {output.tree} \
--method raxml \
--nthreads {threads} 2>&1 | tee {log}
--nthreads {threads:q} 2>&1 | tee {log}
"""

rule refine:
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5 changes: 2 additions & 3 deletions phylogenetic/rules/prepare_sequences.smk
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Expand Up @@ -61,14 +61,13 @@ rule align:
"logs/align.txt",
benchmark:
"benchmarks/align.txt"
params:
threads = workflow.cores
threads: workflow.cores
shell:
"""
augur align \
--sequences {input.sequences} \
--output {output.alignment} \
--fill-gaps \
--reference-sequence {input.reference} \
--nthreads {threads} 2>&1 | tee {log}
--nthreads {threads:q} 2>&1 | tee {log}
"""