Productivity

tools-only Bundle

Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution. Use when creating Python-based workflows, automating multi-step analyses with make-like dependency tracking, or running pipelines on HPC clusters with SLURM.

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End of day review with learning capture, daily plan completion tracking, and meeting follow-up surfacing.

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Full Board of Directors deliberation with 5 expert directors assessing, discussing, and voting.

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Get current time, timezone info, and meeting scheduler for any location worldwide

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Strategic task planning and breakdown specialist for complex development work

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End-to-end YouTube publishing workflow using ordered scripts: prepare/concat video, upload draft, transcribe with Parakeet, generate copy+thumbnails with Gemini, update YouTube metadata, then schedule socials (Postiz) 15 minutes after publish.

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Search .flow/memory/ for entries relevant to the current task or request.

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Ephemeral worker for executing a single task. Coordinates via message bus.

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Process synced Granola meetings to update person pages, extract tasks, and organize meeting notes

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Task-agnostic autonomous execution. Identifies any task and executes it through a complete fix-verify loop until done. Use when asked to "go do", "just do it", "execute this", "/melt", "/build" (legacy), "/forge" (legacy), or "/godo" (legacy).

tools-only Bundle

Generate context-aware daily plan with calendar, tasks, and priorities. Includes midweek awareness, meeting intelligence, commitment tracking, and smart scheduling suggestions.

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Query and manage feature implementation task status. Provides CLI tools to list features, check task status, find ready tasks, and validate task files. Used by /execution orchestrator to track progress. Automatically updates task timestamps via hooks on /start-task.

tools-only Bundle

Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes using WGCNA and CEMiTool. Detects hub genes and module-trait relationships from bulk or single-cell expression data. Use when finding co-expression modules, identifying hub genes, or relating gene networks to clinical or experimental variables.

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Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing to community workflow registries.

tools-only Bundle

Screen S&P 500 stocks for Mark Minervini's Volatility Contraction Pattern (VCP). Identifies Stage 2 uptrend stocks forming tight bases with contracting volatility near breakout pivot points. Use when user requests VCP screening, Minervini-style setups, tight base patterns, volatility contraction breakout candidates, or Stage 2 momentum stock scanning.

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TerminalBench evaluates AI agents on practical terminal and shell tasks including file manipulation, system administration, scripting, and command-line tool usage with validation-command-based evaluation.

tools-only Bundle

Use when a refactoring task file exists from /assessor and tasks need execution. Reads task files, resolves dependencies, delegates to specialist agents (SKILL_SPLIT, AGENT_OPTIMIZE, DOC_IMPROVE), and tracks completion with parallel orchestration

tools-only Bundle

Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

tools-only Bundle

Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches. Use when extracting protein abundances from MS data for differential analysis.

tools-only Bundle

Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R). Essential QC step before clustering to avoid artificial cell populations. Use when identifying and removing doublets from scRNA-seq data.

tools-only Bundle

Expert YARA rule authoring, review, and optimization. Use when writing new YARA rules, reviewing existing rules for quality issues, optimizing rule performance, or converting detection logic to YARA syntax. Covers rule naming conventions, string selection, condition optimization, performance tuning, and automated quality checks based on yaraQA.

tools-only Bundle

Trace downstream data lineage and impact analysis. Use when the user asks what depends on this data, what breaks if something changes, downstream dependencies, or needs to assess change risk before modifying a table or DAG.

tools-only Bundle

Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.

tools-only Bundle

Start or complete a specific task inside a SAM task file. Updates task status to IN PROGRESS with Started timestamp, writes active-task context for hooks, and supports --complete to mark tasks complete.

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DSL and CLI for building and running Agentic Trajectories (ATaC).

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Iterate on a PR until CI passes. Use when you need to fix CI failures, address review feedback, or continuously push fixes until all checks are green. Automates the feedback-fix-push-wait cycle.

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When writing a git commit message. When task completes and changes need committing. When project uses semantic-release, commitizen, git-cliff. When choosing between feat/fix/chore/docs types. When indicating breaking changes. When generating changelogs from commit history.

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Self-Correction and Verification

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Set up comprehensive feature development task with proper tracking

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Validate plugin refactoring completeness — verifies task completion, plugin structure integrity, and regression absence. Use when refactoring results need verification, when checking refactoring goals were achieved without content loss, when checking for regressions after changes, or when validating plugin structure after systematic improvements. Runs plugin_validator.py and generates comprehensive validation reports with quality metrics.

tools-only Bundle

Updates task context manifest with discoveries from current work session. Analyzes implementation code and task file to understand what was learned. Only updates if drift or new discoveries found. Provide the task file path.

tools-only Bundle

Updates task context manifest with discoveries from current work session. Analyzes implementation code and task file to understand what was learned. Only updates if drift or new discoveries found. Provide the task file path.

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Skills Directory Architecture

tools-only Bundle

Browser automation CLI for AI agents. Use when the user needs to interact with websites, including navigating pages, filling forms, clicking buttons, taking screenshots, extracting data, testing web apps, or automating any browser task. Triggers include requests to "open a website", "fill out a form", "click a button", "take a screenshot", "scrape data from a page", "test this web app", "login to a site", "automate browser actions", or any task requiring programmatic web interaction.

tools-only Bundle

Visual Review Workflow for Presentations

tools-only Bundle

flexport-rate-limits