Container Environments

Container Environments

This pipeline uses three main Apptainer/Singularity containers:

meth-analysis.def

• Base: rocker/r-ver:4.4.3
• Purpose: R & Python-based DNAm analysis
• Key tools: methylKit, meffonym, ewaff, pandas, numpy

wgbs-analysis.def

• Base: condaforge/mambaforge:latest
• Purpose: WGBS tools
• Key tools: Bismark, Bowtie2, Methyldackel, Sambamba, Samtools

qc-container.def

• Base: rocker/r-ver:4.4.1
• Purpose: R+Quarto reporting
• Key tools: Quarto, ggplot2, dplyr, data.table

Building Containers

apptainer build meth_analysis.sif meth-analysis.def
apptainer build wgbs_analysis.sif wgbs-analysis.def
apptainer build qc_container.sif qc-container.def