Container

Pre-built container images include Nextflow, papa2, cutadapt, MAFFT, and FastTree — everything needed to run the full pipeline without installing dependencies.

Docker

# Pull the image
docker pull ghcr.io/rec3141/danaseq-illumina-amplicon:latest

# Run the pipeline
docker run --rm -v $(pwd):/data ghcr.io/rec3141/danaseq-illumina-amplicon \
    run /pipeline/main.nf \
    --input /data/reads \
    --ref_databases "silva:/data/silva.fasta:Domain,Phylum,Class,Order,Family,Genus" \
    --outdir /data/results \
    -resume

Apptainer (HPC)

# Pull and convert to SIF
apptainer pull danaseq-illumina-amplicon.sif docker://ghcr.io/rec3141/danaseq-illumina-amplicon:latest

# Run the pipeline
apptainer exec danaseq-illumina-amplicon.sif nextflow run /pipeline/main.nf \
    --input /path/to/reads \
    --ref_databases "silva:/path/to/silva.fasta:Domain,Phylum,Class,Order,Family,Genus" \
    --outdir results \
    -resume

Nextflow with Container Profile

Nextflow can pull and manage the container automatically:

# Docker
nextflow run rec3141/danaSeq -entry illumina_amplicon \
    --input /path/to/reads \
    --ref_databases "silva:/path/to/silva.fasta:Domain,Phylum,Class,Order,Family,Genus" \
    -with-docker ghcr.io/rec3141/danaseq-illumina-amplicon:latest \
    -resume

# Singularity/Apptainer
nextflow run rec3141/danaSeq -entry illumina_amplicon \
    --input /path/to/reads \
    --ref_databases "silva:/path/to/silva.fasta:Domain,Phylum,Class,Order,Family,Genus" \
    -with-singularity docker://ghcr.io/rec3141/danaseq-illumina-amplicon:latest \
    -resume

What's Inside

The container includes both Python and R environments:

Component	Version	Source
Nextflow	latest	nextflow.io
papa2	0.1.0	bioconda
cutadapt	latest	bioconda
MAFFT	latest	bioconda
R + dada2	4.x + 1.36	bioconda

Building Locally

git clone https://github.com/rec3141/danaSeq.git
cd danaSeq/illumina_amplicon
docker build -t danaseq-illumina-amplicon illumina_amplicon