Tencent Health Omics Task Analysis

Problem

omics-task-skill is for engineers operating the Tencent Health Omics platform through omics-platform-cli. It addresses repetitive CLI flag construction, auth failures, incomplete local configuration, unclear public-app import semantics, and unknown trial quota before running tasks. It maps common requests to whitelisted commands and enforces confirmation before execution.

How it works

The skill first checks whether the CLI is installed, then runs omics whoami and omics config show to verify login state and project, environment, and COS bucket settings. If authentication fails, it initiates omics login; if configuration is missing, it guides the user through B-side or C-side setup. Query capabilities include list public-apps, list apps, list versions, list templates, and list volume. Run operations only use omics run with one of four mutually exclusive forms: --wdl, --nf, --public-app, or --app. Before invoking run, the skill assembles the full command, prints a parameter summary, and requires explicit user confirmation; C-side trial users must also pass omics quota first. For failures, omics status and omics debug can inspect subtasks and stderr.

Boundaries

The skill may only call whitelisted commands and must not bypass the CLI to access backend APIs, SQL, or the filesystem. Public app collections cannot be run directly; their sub-apps must be expanded and selected first. Form B requires an explicit --app-type, form D rejects --update, and C-side accounts cannot use local WDL or COS Nextflow forms. If parameter merging fails, follow the PARAM_MERGE_FAILED details to supply required values before retrying.