The Agent Skills Directory

[COMMAND_EXECUTION]: The helper script scripts/run_pacsomatic.py performs multiple system calls using subprocess.run to interact with environment managers (conda, mamba), version control (git), and runtime environments (java, nextflow). It also executes HPC scheduler commands like bsub, sbatch, and qsub to submit tasks.
[EXTERNAL_DOWNLOADS]: The skill is configured to clone the official nf-core/pacsomatic pipeline from GitHub (https://github.com/nf-core/pacsomatic.git) if a local copy is not provided. It also supports the automatic creation of Conda environments from YAML specification files, which involves downloading packages from remote registries.
[REMOTE_CODE_EXECUTION]: The skill dynamically generates shell scripts containing Nextflow commands and scheduler directives. These scripts are subsequently executed on the host system or an HPC cluster. Input sanitization is performed using shlex.quote for most parameters to mitigate shell injection risks, though the --module-load parameter is included in the generated script as a raw string without explicit sanitization.

pacsomatic