
This report describes work carried out for ELIXIR Norway ELIXIR3 Deliverable D5.6: “Implementation of existing workflows and toolkits for sensitive computing.” The report documents the transition from framework to practical implementation by confirming that the Galaxy CVMFS BioContainers repository is available inside the TSD/Colossus secure computing environment. The work demonstrates that externally maintained BioContainers can be accessed under /cvmfs/singularity.galaxyproject.org/all and executed through Apptainer on the Colossus submit host. An existing ATAC-seq Snakemake workflow was used as a representative workflow/toolkit to validate the approach. Initial workflow stages, including setup and raw-data quality control with FastQC and MultiQC, were successfully executed using CVMFS-hosted BioContainers. The result shows that existing containerized workflows can be adapted for execution inside secure computing environments while keeping sensitive data inside the Trusted Research Environment.
