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Remove redundant include strains #843

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Remove redundant include strains #843

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3692aeb
Remove redundant include strains
huddlej Jan 25, 2022
9edf570
Define list of strains to ignore for proximities
huddlej Jan 25, 2022
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1 change: 0 additions & 1 deletion defaults/include.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,2 @@
Wuhan/Hu-1/2019
Wuhan-Hu-1/2019
Wuhan/WH01/2019
4 changes: 4 additions & 0 deletions defaults/parameters.yaml
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Expand Up @@ -89,8 +89,12 @@ filter:
# will help reduce the number of genetically identical strains that get chosen,
# and allows for more diversity represented on the tree.
priorities:
ignore_sequences:
- Wuhan/Hu-1/2019
- Wuhan-Hu-1/2019
crowding_penalty: 0.1


# Alignment settings
# Alignments are partitioned into smaller groups to speed up the overall alignment process.
# The number of sequences per group determines the run time of a single alignment job.
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2 changes: 1 addition & 1 deletion workflow/snakemake_rules/main_workflow.smk
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Expand Up @@ -369,7 +369,7 @@ rule proximity_score:
"benchmarks/proximity_score_{build_name}_{focus}.txt"
params:
chunk_size=10000,
ignore_seqs = config['refine']['root']
ignore_seqs = config['priorities']['ignore_sequences'],
resources:
# Memory scales at ~0.15 MB * chunk_size (e.g., 0.15 MB * 10000 = 1.5GB).
mem_mb=4000
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