The Agent Skills Directory

[COMMAND_EXECUTION]: The main helper script scripts/run_pacsomatic.py executes various system commands to manage the execution environment and pipeline run.
It uses subprocess to check the version of java and to manage conda or mamba environments.
It optionally clones the pipeline repository using git if a local checkout is not provided.
It invokes Nextflow to execute the bioinformatics pipeline.
[COMMAND_EXECUTION]: The skill facilitates interaction with HPC job schedulers.
It generates and submits launch scripts using scheduler-specific commands such as bsub (LSF), sbatch (Slurm), and qsub (PBS/SGE).
The commands are constructed using shlex.quote to prevent command injection from file paths.
[EXTERNAL_DOWNLOADS]: The skill is designed to download the nf-core/pacsomatic pipeline code and associated test datasets from the official nf-core GitHub repository.
[REMOTE_CODE_EXECUTION]: By design, the skill executes Nextflow pipelines, which are remote-origin scripts. This is the primary and intended functionality of the skill for performing genomic analysis.

pacsomatic