sd_ww_processing

repo for data storage and shared analyses

Instructions

Set number of parallel jobs to run in demix_parallel_ubuntu.sh. Default is set to 30.

To run use the docker container,

docker build -t condaforge/miniforge3:freyja-2.0.0 .
docker run -v $(pwd):/data condaforge/miniforge3:freyja-2.0.0

Name		Name	Last commit message	Last commit date
Latest commit History 83 Commits
depths		depths
outputs		outputs
variants		variants
.gitignore		.gitignore
241212_SG_WW-freyja-metadata.csv		241212_SG_WW-freyja-metadata.csv
Dockerfile		Dockerfile
Encina_sewage_seqs.csv		Encina_sewage_seqs.csv
NC_045512_Hu-1.fasta		NC_045512_Hu-1.fasta
NC_045512_Hu-1.fasta.fai		NC_045512_Hu-1.fasta.fai
PointLoma_sewage_seqs.csv		PointLoma_sewage_seqs.csv
README.md		README.md
SouthBay_sewage_seqs.csv		SouthBay_sewage_seqs.csv
agg_outputs.tsv		agg_outputs.tsv
all-ww-metadata.csv		all-ww-metadata.csv
calc_relgrowthrates.py		calc_relgrowthrates.py
call_var.sh		call_var.sh
demix_parallel.sh		demix_parallel.sh
demix_parallel_ubuntu.sh		demix_parallel_ubuntu.sh
entrypoint.sh		entrypoint.sh
get_data_aws.sh		get_data_aws.sh
get_metadata0.py		get_metadata0.py
last_barcode_update.txt		last_barcode_update.txt
lineages.yml		lineages.yml
links.txt		links.txt
pathogen_config.yml		pathogen_config.yml
plot_config.yml		plot_config.yml
polish_outputs.py		polish_outputs.py
rel_growth_rates.csv		rel_growth_rates.csv
usher_barcodes.feather		usher_barcodes.feather