This sub-skill provides a concise preflight troubleshooting checklist for running Nextflow pipelines that depend on Docker and Java. It verifies common fai…
This sub-skill provides a concise preflight troubleshooting checklist for running Nextflow pipelines that depend on Docker and Java. It verifies common failure points and gives exact remediation commands: install Docker (https://docs.docker.com/get-docker/), fix permission issues with sudo usermod -aG docker $USER and re-login, start the Docker daemon with sudo systemctl start docker, install Nextflow via curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ and update with nextflow self-update, and ensure Java 11 with sudo apt install openjdk-11-jdk. Use this skill before executing pipelines (local, cloud, or HPC) to prevent runtime failures. Core advantages: fast, actionable fixes; minimal commands; clear gate—"Do not proceed until all checks pass"—and a pointer to HPC/Singularity troubleshooting in references/troubleshooting.md.
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