Monitor snakemake and nextflow pipelines, detect errors, and restart failed jobs.
npx skills add https://github.com/genomewalker/cc-soul --skill shepherd-genomewalker
Please help me install this Agent Skill. Skill: shepherd Source: https://github.com/genomewalker/cc-soul/tree/main/skills/shepherd Command: npx skills add https://github.com/genomewalker/cc-soul --skill shepherd-genomewalker
This Skill automates the monitoring and management of long-running bioinformatics pipelines, preventing failures and ensuring continuous progress without constant human oversight.
Start monitoring a snakemake pipeline with a 60-second check interval and a maximum of 3 restarts.
High-intent search queries and answers about installing and using this skill.
Automate pipeline monitoring by running an autonomous sense-think-act loop that detects errors, recalls fixes from memory, and restarts failed jobs up to a configurable limit. It prevents long-running bioinformatics pipelines from stalling due to transient network or resource issues.
Handling transient pipeline errors involves detecting failures and automatically applying learned fixes from memory before restarting the job. This approach ensures continuous progress for multi-day genomic analyses without requiring constant human oversight.
Yes, you can run pipelines in isolated Zellij sessions for enhanced reliability. Session management ensures robust task execution and isolation, preventing pipeline interruptions from affecting other operations.
Yes, autonomous monitoring works with both snakemake and nextflow pipelines. It uses a sense-think-act loop to detect errors, recall previous fixes, and restart failed jobs within isolated Zellij sessions.
Configure automated pipeline monitoring by setting a specific check interval, such as 60 seconds, and defining a maximum number of restart attempts. The monitor will restart failed jobs automatically up to this limit before requesting manual intervention.
Isolated Zellij sessions provide enhanced reliability for pipeline management by ensuring robust execution environments. Utilizing chitta and zellij-mcp tools for task execution prevents pipeline failures from impacting the broader system.
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