Productivity skills

Coordinator-only native Codex issue-to-develop workflow. Specialists use only their assigned role and task.

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Use when working with the Resend email API — sending transactional emails (single or batch), receiving inbound emails via webhooks, managing email templates, tracking delivery events, managing domains, contacts, broadcasts, webhooks, API keys, automations, events, viewing API request logs, or setting up the Resend SDK. Always use this skill when the user mentions Resend, even for simple tasks like "send an email with Resend" — the skill contains critical gotchas (idempotency keys, webhook verification, template variable syntax) that prevent common production issues.

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Use when adding durable execution to a TypeScript project — building retry-safe webhook handlers, background jobs that survive crashes, scheduled tasks, or long-running workflows that outlive a single request. Covers Inngest SDK installation, client config, environment variables, serve endpoints (Next.js, Express, Hono, Fastify), connect-as-worker mode, and the local dev server.

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Use when implementing delays that must survive process restarts (e.g., 24-hour cart abandonment, scheduled follow-ups), waiting for human approval or external events with timeouts (review gates, webhook callbacks, async API completion), polling external services without losing state on crashes, calling other functions and awaiting their results, memoizing expensive operations so they don't re-run on retry, or running async work in parallel inside a workflow. Covers Inngest step methods: step.run, step.sleep, step.waitForEvent, step.waitForSignal, step.sendEvent, step.invoke, step.ai, plus patterns for loops and parallel execution.

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Grill me about specs for the workflows I want to build, within this workspace.

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Use when building durable AI agents or agentic workflows with Inngest and AgentKit, including model calls, tool calls, multi-agent networks, human approval, realtime progress, provider rate limits, crash-safe execution, and Agent Evals handoff. Covers AgentKit, `step.ai`, `step.run`, `step.waitForEvent`, native realtime, and when to use lower-level Inngest primitives instead of an in-memory agent loop. Use `inngest-agent-evals` with this skill when the user wants scoring, sessions, experiments, deferred scorers, or outcome-based evaluation for the agent.

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Execute via @babysitter. Use this skill when asked to babysit a task, do anything that is structured process-driven (even a loop) or whenever it is called explicitly. (babysit, babysitter, with a process, orchestrate, orchestrate a run, workflow, loop until, etc.)

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Use when building any system where email content triggers actions — AI agent inboxes, automated support handlers, email-to-task pipelines, or any workflow processing untrusted inbound email. Always use this skill when the user wants to receive emails and act on them programmatically, even if they don't mention "agent" — the skill contains critical security patterns (sender allowlists, content filtering, sandboxed processing) that prevent untrusted email from controlling your system.

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Use when building email features, emails going to spam, high bounce rates, setting up SPF/DKIM/DMARC authentication, implementing email capture, ensuring compliance (CAN-SPAM, GDPR, CASL), handling webhooks, retry logic, making emails accessible (alt text, headings, contrast, screen readers), or deciding transactional vs marketing.

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Create a Conventional Commit message for staged changes and run git commit. Use when changes are staged and you need a commit message in the form type(scope): subject, with a <=100 character imperative header and optional 'ref AL-###' body line. Retained for reference; use only when explicitly asked for this commit workflow.

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Maintain the canonical TASKS.csv with permanent IDs, provenance and lifecycle history; list, add, update, complete, cancel or import selected actions.

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Suggest complementary products that pair well with a given item — side tables for sofas, task lights for desks, etc. Use when the user asks "what goes with" a product, wants coordinating pieces, or asks to complete a furniture grouping.

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Help users connect Arch Studio, understand its access and memory, choose a first workflow, and troubleshoot from reported evidence. General architecture and project execution stays with its owning skill.

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Turn supplied meeting notes or transcripts into sourced minutes, keeping discussion, statements, confirmed/proposed decisions and proposed actions distinct.

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Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions). Covers detecting raw VCFs via FILTER column and QUAL inspection, QUAL-based filtering with bcftools, Ts/Tv interpretation, and when NOT to filter. Read before any variant-level QC task. See bcftools-variant-manipulation for advanced filters, gatk-variant-calling for caller config, samtools-bam-processing for upstream alignment QC.

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Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common counting mistakes. Use when running BUSCO QC, comparing assemblies, or reporting completeness. See also: prokka-genome-annotation for annotation workflows feeding BUSCO.

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Pythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, fingerprints, similarity, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformers, and visualization. Returns native rdkit.Chem.Mol. Prefer datamol for standard workflows; use RDKit directly for advanced control.

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smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (--custom_scoring), local optimization of an existing pose (--local_only), per-atom contributions (--atom_term_data), or SDF/MOL2 ligands without manual PDBQT conversion. For unknown binding sites use diffdock; for the Python-bindings/Vinardo workflow use autodock-vina-docking.

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Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required. Search by name/CID/SMILES/InChIKey/formula, retrieve properties (MW, XLogP, TPSA, H-bond counts), do similarity/substructure searches with async ListKey polling, fetch synonyms, descriptions, assay summaries, and download SDF/PNG. For local cheminformatics use rdkit; for bioactivity-centric workflows use chembl-database-bioactivity.

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Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.

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Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for rule-based Python workflows; use Nextflow for containerized, cloud-native, and nf-core pipelines.

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Unified Python framework for extracellular electrophysiology. Load 20+ formats (SpikeGLX, OpenEphys, NWB, Intan, Maxwell, Blackrock), preprocess, run 10+ sorters (Kilosort4, SpykingCircus2, Tridesclous, MountainSort5) via one API, compute quality metrics (SNR, ISI, firing rate), compare sorters, export NWB/Phy. For format-agnostic multi-sorter workflows. For Neuropixels-specific PSTH/decoding use neuropixels.

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Python-based workflow manager for reproducible, scalable pipelines. Define rules with file-based dependencies; Snakemake resolves execution order and parallelism. Runs local, SLURM, LSF, AWS, GCP via profiles; per-rule conda/Singularity envs. For NGS pipelines, ML training, and multi-step file processing. Use Nextflow for Groovy dataflow or nf-core integration.

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Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons OT-2, or a simulator without vendor lock-in. For protocol automation, method dev, plate reformatting, serial dilutions, and Python lab workflows.

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