The Agent Skills Directory

[COMMAND_EXECUTION]: The script scripts/run_pacsomatic.py uses subprocess.run to interact with system tools such as java, git, and HPC schedulers (sbatch, bsub, qsub). These calls are necessary for the tool's primary purpose and use shlex.quote for parameter sanitization.
[EXTERNAL_DOWNLOADS]: The skill facilitates the cloning of the nf-core/pacsomatic repository from GitHub. This is a standard and expected behavior for using this specific scientific pipeline.
[SAFE]: The skill generates execution scripts and samplesheets dynamically. It performs specific validation on identifiers (e.g., checking for spaces) and uses proper quoting for all paths interpolated into shell scripts, minimizing the risk of accidental or malicious command injection.

pacsomatic