Container¶

Pre-built container images include Nextflow, papa2, microscape, cutadapt, MAFFT, and R/dada2 — everything needed to run the full pipeline without installing dependencies.

Docker¶

# Pull the image
docker pull ghcr.io/rec3141/microscape-nf:latest

# Run the pipeline
docker run --rm -v $(pwd):/data ghcr.io/rec3141/microscape-nf \
    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 microscape-nf.sif docker://ghcr.io/rec3141/microscape-nf:latest

# Run the pipeline
apptainer exec microscape-nf.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/microscape-nf \
    --input /path/to/reads \
    --ref_databases "silva:/path/to/silva.fasta:Domain,Phylum,Class,Order,Family,Genus" \
    -with-docker ghcr.io/rec3141/microscape-nf:latest \
    -resume

# Singularity/Apptainer
nextflow run rec3141/microscape-nf \
    --input /path/to/reads \
    --ref_databases "silva:/path/to/silva.fasta:Domain,Phylum,Class,Order,Family,Genus" \
    -with-singularity docker://ghcr.io/rec3141/microscape-nf: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
microscape	0.1.0	bioconda
cutadapt	latest	bioconda
MAFFT	latest	bioconda
R + dada2	4.x + 1.36	bioconda
microscapeR	0.99.0	GitHub

Building Locally¶

git clone https://github.com/rec3141/microscape-nf.git
cd microscape-nf
docker build -t microscape-nf .