Update resources and download commands
Resolves conflicts with master
@@ -6,8 +6,8 @@ rule download:
conda: config["conda_environment"]
shell:
"""
- aws s3 cp s3://nextstrain-ncov-private/metadata.tsv {output.metadata:q}
- aws s3 cp s3://nextstrain-ncov-private/sequences.fasta {output.sequences:q}
+ aws s3 cp s3://nextstrain-ncov-private/metadata.tsv.gz - | gunzip -cq >{output.metadata:q}
+ aws s3 cp s3://nextstrain-ncov-private/sequences.fasta.gz - | gunzip -cq > {output.sequences:q}
"""
rule filter:
@@ -314,10 +314,10 @@ rule refine:
"benchmarks/refine_{region}.txt"
threads: 1
resources:
- # Multiple sequence alignments can use up to 40 times their disk size in
- # memory, especially for larger alignments.
+ # Multiple sequence alignments can use up to 15 times their disk size in
+ # memory.
# Note that Snakemake >5.10.0 supports input.size_mb to avoid converting from bytes to MB.
- mem_mb=lambda wildcards, input: 40 * int(input.size / 1024 / 1024)
+ mem_mb=lambda wildcards, input: 15 * int(input.size / 1024 / 1024)
params:
root = config["refine"]["root"],
clock_rate = config["refine"]["clock_rate"],
