Bacterial Genomics

General schematic of the steps in the workflow

Requirements

• Nextflow (>=22.04.3)
• Docker or Singularity (>=3.8.0)

Install workflow locally

git clone https://github.com/bacterial-genomics/wf-paired-end-illumina-assembly.git

Run workflow

Before running workflow on new data, the workflow should be run on the built-in test data to make sure everything is working properly. It will also download all dependencies to make subsequent runs much faster.

cd wf-paired-end-illumina-assembly/

nextflow run main.nf -profile singularity,test --outdir results

Usage

nextflow run main.nf \
  -profile singularity \
  --input INPUT_DIRECTORY \
  --outdir OUTPUT_DIRECTORY \
  --assembler <spades|skesa>

When running locally, --max_cpus and --max_memory may need to be specified. Below, max CPUs is set to 4 and max memory is set to 16 (for 16GB).

nextflow run main.nf \
  -profile singularity \
  --input INPUT_DIRECTORY \
  --outdir OUTPUT_DIRECTORY \
  --max_cpus 4 \
  --max_memory 16

Help menu of all options

nextflow run main.nf --help

Test data was generated by taking top 1 million lines (=250k reads) of SRA data SRR16343585. (Note: This requires SRA Toolkit)

fasterq-dump SRR16343585
head -1000000 SRR16343585_1.fastq > test_R1.fastq
head -1000000 SRR16343585_2.fastq > test_R2.fastq
pigz test_R{1,2}.fastq