1. Quick Start

Important

BigBacter requires Nextflow and one of the following container engines: Docker, Podman, Apptainer, Singularity.

1. Configure your PopPUNK database (Performed once per species):

Note

This example shows how to configure the E. coli database. You can find a list of available PopPUNK databases here and instructions for how to add your own databases here.

nextflow run DOH-JDJ0303/bigbacter-nf \
    -r main \
    -profile docker,Escherichia_coli_db \
    -entry PREPARE_DB \
    --db $PWD/db

2. Prepare your samplesheet (Performed each time):

Note

Nextflow requires the use of absolute file paths in samplesheets.

samplesheet.csv:

sample,taxa,assembly,fastq_1,fastq_2
sample1,Acinetobacter_baumannii,sample1.fasta,sample1_R1.fastq.gz,sample1_R2.fastq.gz
sample2,Escherichia_coli,sample2.fasta,sample2_R1.fastq.gz,sample2_R2.fastq.gz
sample3,Staphylococcus_aureus,sample3.fasta,sample3_R1.fastq.gz,sample3_R2.fastq.gz

3. Running BigBacter (Performed each time):

Note

Nextflow versions ≥ 23.10 require that you run export NXF_SINGULARITY_HOME_MOUNT=true when running with -profile singularity or Gubbins will fail (issue 7).

nextflow run DOH-JDJ0303/bigbacter-nf \
    -r main \
    -profile docker \
    --input $PWD/samplesheet.csv
    --db $PWD/db \
    --outdir $PWD/results \
    --max_cpus 4 \
    --max_memory 8.GB

4. Add the new samples to your database (Performed each time):

Note

This is the same command as step 3 but with -resume and --push true.

nextflow run DOH-JDJ0303/bigbacter-nf \
    -r main \
    -profile docker \
    --input $PWD/samplesheet.csv
    --db $PWD/db \
    --outdir $PWD/results \
    --max_cpus 4 \
    --max_memory 8.GB \
    --push true \
    -resume