SARS-CoV-2 build definitions for Africa CDC

Build configuration for Africa CDC SARS-CoV-2 builds hosted at https://nextstrain.org/groups/africa-cdc.

Instructions for running Africa CDC builds with GISAID data

Setup Repositories

git clone https://github.com/nextstrain/ncov-africa-cdc.git
git clone https://github.com/nextstrain/ncov.git
cd ncov
cp -r ../ncov-africa-cdc/africa_cdc_profile .

Download data

Select the “Downloads” link from the EpiCoV navigation bar. Scroll to the “Genomic epidemiology” section and select the “nextregions” button. Select the “Africa” button. Save the file as hcov_africa.tar.gz in the ncov/data/ workflow directory.

Click "Back" to return to the main "Download" dialog, find the “Download packages” section, and select the “FASTA” button. Save the full GISAID sequences as data/sequences_fasta.tar.xz.

Select the “metadata” button from that same “Download packages” section and download the corresponding file as data/metadata_tsv.tar.xz.

Filter data

Navigate to the ncov workflow directory and enter a Nextstrain runtime shell there.

nextstrain shell .

Extract African metadata and sequences from full GISAID downloads.

# Get metadata for Africa directly from tarball.
tar xOf data/metadata_tsv.tar.xz metadata.tsv \
  | tsv-filter -H --str-in-fld Location:Africa \
  | xz -c -2 > data/metadata_africa.tsv.xz

# Get strain names for genomes.
# GISAID uses virus name, collection date, and submission date
# delimited by a pipe character.
xz -c -d data/metadata_africa.tsv.xz \
  | tsv-select -H -f 'Virus\ name','Collection\ date','Submission\ date' \
  | sed 1d \
  | awk -F "\t" '{ print $1"|"$2"|"$3 }' > data/strains_africa.txt

# Get genomes for strain names from tarball.
tar xOf data/sequences_fasta.tar.xz sequences.fasta \
  | seqkit grep --by-name -f data/strains_africa.txt \
  | xz -c -2 > data/sequences_africa.fasta.xz

Run builds locally

Navigate to the ncov workflow directory; these instructions assume this is a sibling directory to this repository. By default, the following command will run builds for all countries and regions.

nextstrain build \
  --cpus 4 \
  --memory 8Gib \
  . \
  --configfile ../ncov-africa-cdc/builds_africa.yaml

You can specify a comma-delimited subset of builds to run by build name. The following example only runs builds for Ghana and Kenya.

nextstrain build \
  --cpus 4 \
  --memory 8Gib \
  . \
  --configfile ../ncov-africa-cdc/builds_africa.yaml \
  --config active_builds=ghana,kenya

Run builds on AWS Batch

To run builds on AWS Batch, the build config and profiles directory must be in the ncov workflow directory. Sync those files into ncov.

# Run from ncov/
rsync -arvz \
  ../ncov-africa-cdc/builds_africa.yaml \
  ../ncov-africa-cdc/africa_cdc_profile \
  .

Run all builds on AWS Batch.

nextstrain build \
  --aws-batch \
  --cpus 36 \
  --memory 70Gib \
  . \
  --configfile builds_africa.yaml

Run builds on Terra

TBD.

nextstrain / ncov-africa-cdc

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