SarahNadeau / burk-nextstrain

An automated nextstrain build for Burkholderia pseudomallei

Burkholderia pseudomallei automated Nextstrain build

This project is to keep a Nextstrain build for B. pseudomallei automatically updated whenever new data is made available in NCBI's RefSeq database.

Requirements:

• Environment variable NCBI_API_KEY: API key for querying NCBI. To get a key, follow the instructions here.
• Environment variable NCBI_EMAIL: email address to be associated with queries to NCBI.
• Python3 with pandas installed.

To download data and run a small example:

nextflow run \
    -profile docker \
    --api_key $NCBI_API_KEY \
    --ncbi_email $NCBI_EMAIL \
    main.nf

To run a small example for B. pseudomallei, first download a reference genome as put it in assets. Here I use GCF_000756125.1 as the reference. This run uses a cached version of the NCBImeta database and only runs the full pipeline on 5 assemblies.

nextflow run main.nf \
    -profile docker \
    -stub-run \
    --api_key $NCBI_API_KEY \
    --ncbi_email $NCBI_EMAIL \
    --ncbimeta_config ncbimeta/b_pseudomallei_refseq.yaml \
    --reference assets/GCF_000756125.1_ASM75612v1_genomic.fna \
    --output_dir burk_results \
    --data_dir assets/burk_data/assemblies \
    --max_assemblies 5

Developer notes

To utilize the Github actions workflows defined in .github/workflows, you need to add two secrets to your repository, NCBI_API_KEY and NCBI_EMAIL.

nextflow run main.nf
-profile docker
-with-report
--api_key $NCBI_API_KEY
--ncbi_email $NCBI_EMAIL
--ncbimeta_config ncbimeta/b_pseudomallei_refseq.yaml
--reference assets/GCF_000756125.1_ASM75612v1_genomic.fna
--output_dir burk_results_5
--data_dir assets/burk_data/assemblies
--max_assemblies 5