The Agent Skills Directory

[COMMAND_EXECUTION]: The helper script scripts/run_pacsomatic.py executes shell commands to submit generated launch scripts to various job schedulers, including LSF, Slurm, PBS, and SGE. The script utilizes shlex.quote to sanitize the script path before constructing the submission command.
[EXTERNAL_DOWNLOADS]: The skill facilitates downloading the pipeline source code from the official nf-core GitHub repository. Additionally, the script is designed to handle bioinformatics data (BAM files) located on remote servers using protocols such as HTTP, HTTPS, S3, GS, and FTP.
[REMOTE_CODE_EXECUTION]: The skill manages the execution of external bioinformatics workflows by generating standalone shell scripts and invoking them through the Nextflow runtime. It also includes functionality to resolve dependencies by creating and activating Conda environments, which involves installing software packages from remote repositories.

pacsomatic