Shovill Nextflow Pipeline

This Nextflow pipeline automates genome assembly using Shovill for paired-end FASTQ reads. It supports both samplesheet input and automatic file pair discovery.

Features

• Runs Shovill assembly on multiple samples in parallel
• Flexible input: CSV samplesheet or automatic FASTQ pairing
• Configurable assembler (SPAdes, SKESA, etc.)
• Multi-threaded processing
• Publishes assembled contigs as ${sample_id}_contigs.fa

Requirements

• Nextflow ≥ 22.10.0
• Shovill (with assembler dependencies)
• Paired-end FASTQ files (.fastq/.fq/.gz)

Usage

nextflow run BCCDC-PHL/nf_shovill \
  --outdir ./results \
  --threads 8 \
  [--samplesheet_input samples.csv] \
  [--fastq_input "path/to/fastq/*_{R1,R2}*.fastq.gz"]

Parameters

Parameter	Default	Description
--outdir	./results	Output directory
--threads	8	CPU threads per sample
--assembler	skesa	Shovill assembler (spades, skesa, megahit)
--samplesheet_input	NO_FILE	CSV samplesheet path
--fastq_input	Required if no samplesheet	FASTQ search pattern

Output

sample1/
├── sample1_contigs.fa
├── sample1_shovill.log
├── sample1_shovill_provenance.yml
└── 
...