DevOps & Infra

gptomics Bundle

Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware alignment (NO deduplication for non-UMI MeRIP), deepTools replicate-concordance + IP-enrichment QC, PreSeq saturation curves, exomePeak2 (transcript-aware, GC-bias-aware negative-binomial GLM) peak calling, optional MACS3 broad-peak cross-check, DRACH motif confirmation as a sanity check (NOT a per-peak filter), exomePeak2 differential calling via the four-BAM-vector interface (bam_ip + bam_input control; bam_treated_ip + bam_treated_input treatment), ChIPseeker annotation, and the canonical Guitar metagene with stop-codon enrichment as the biological QC anchor. Use when running a complete MeRIP analysis from raw reads, when chaining the constituent epitranscriptomics skills (merip-preprocessing -> m6a-peak-calling -> m6a-differential -> modification-visualization), or when wrapping the pipeline in Snakemake / Nextflow.

ariffazil Skill

OpenClaw-native /propose-seal — proposes a sealed candidate to 888-APEX. NEVER self-seals. Pipeline: agent proposes → 888 judges → F13 authorizes → 999 executes (append to VAULT999).

ariffazil Skill

OpenCode-native /propose-seal — proposes a sealed candidate to 888-APEX after a code mutation. NEVER self-seals. Pipeline: OpenCode compiles evidence → 888 judges → F13 authorizes → 999 appends to VAULT999.

ariffazil Bundle

Build GitHub Actions CI/CD pipelines, Docker multi-stage builds, and deploy-verify patterns for VPS af-forge.

ariffazil Skill

Real-time Caddy HTTP error spike monitor, Docker container log stream analyzer, and automated container health recovery watchdog.

gptomics Bundle

Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (FeatureTable[Frequency], SampleData[PairedEndSequencesWithQuality], Phylogeny[Rooted], FeatureData[Taxonomy]), embedded provenance plus provenance replay, import (Casava/manifest/EMP/BIOM), export, the Metadata object, and the q2cli vs Artifact API interfaces. Covers why a .qza is data-plus-executable-history not a file, why export drops provenance, why a .qzv is terminal, why classifier .qza are version-pinned, and the 2026 distribution/rachis rename. Use when importing reads, choosing a manifest/Casava/EMP/BIOM path, reading or replaying provenance, exporting to BIOM/phyloseq, fixing semantic-type or Phred or sklearn-version errors, or orchestrating the pipeline. Denoising -> amplicon-processing; classifier/DB -> taxonomy-assignment; diversity metric/depth -> diversity-analysis; DA tool -> differential-abundance; PICRUSt2 -> functional-prediction; shotgun moshpit -> metagenomics.

oimiragieo Bundle

Evaluates completed agent pipelines across 5 scoring dimensions and produces a composite verdict with actionable recommendations

ariffazil Skill

Full VPS Docker status — all containers, resource usage, arifOS health. Use when Arif asks about container status, VPS health, what's running, memory/CPU usage, or wants to restart/rebuild services.

gptomics Bundle

End-to-end Ribo-seq analysis from FASTQ through periodicity QC, P-site calibration, ORF detection, translation efficiency, and stalling. Use when orchestrating a full ribosome profiling pipeline and deciding harvest/dedup/alignment options and which downstream analyses the library can support.

oimiragieo Bundle

6-phase multi-agent pipeline with approval gates. Orchestrates Plan→Design→Implement→Review→Test→Deploy phases with explicit entry/exit criteria, phase-level agent assignment, and human-in-the-loop approval checkpoints.

oimiragieo Bundle

Cloud and DevOps expert including AWS, GCP, Azure, and Terraform

ariffazil Bundle

Monitor and manage the arifOS federation: docker compose ps, restart dead services, MCP health probes (Observed Port Map), container drift detection, restart count monitoring. USE WHEN: "federation status", "restart dead container", "container health", "docker drift", "service down", "probe MCP", "health check federation". Runs on af-forge (VPS) — native docker and curl required.

ariffazil Skill

Invoke arifOS constitutional MCP tools (000-999 pipeline, F1-F13 enforced). Use to call arif_* tools on the arifos_remote MCP server.

gptomics Bundle

Calls germline SNPs and indels with Google DeepVariant, which reframes variant calling as CNN image classification over multi-channel pileup tensors. Covers platform-specific model selection (WGS, WES, PACBIO, ONT_R104, HYBRID_PACBIO_ILLUMINA), one-shot run_deepvariant vs the three-stage make_examples/call_variants/postprocess_variants pipeline, GPU acceleration of call_variants, DeepTrio for family/trio and de-novo calling, and joint genotyping of gVCFs with GLnexus (not GenotypeGVCFs). Use when deciding DeepVariant vs GATK vs DRAGEN, picking the right --model_type for a sequencing platform, avoiding post-hoc GATK hard filters or BQSR that degrade CNN calls, calling de-novo variants in a trio, merging a DeepVariant cohort, or weighing GIAB-trained benchmark accuracy before clinical deployment.

sboghossian-mini-claude-for-legal Skill

Use when an enterprise customer's IT administrator needs to configure Single Sign-On (SSO) for Louis using SAML 2.0 with their identity provider (Okta, Azure AD / Entra ID, Google Workspace, or Auth0). Covers the end-to-end setup flow, attribute mapping, tenant and group provisioning, testing, and rollout. Applicable across all jurisdictions for any Enterprise-tier deployment.

sboghossian-mini-claude-for-legal Skill

Use when an error occurs anywhere in the legal AI request pipeline and a structured response decision is needed. Classifies errors into six categories (transient, provider, client-input, auth/quota, backend-bug, schema/data-integrity) and outputs the correct action (retry, failover, user guidance, upgrade flow, ticket, escalation) along with a user-facing message and an optional internal ticket reference.

sboghossian-mini-claude-for-legal Skill

Use when a matter involves oil and gas contracts, energy sector licensing, upstream/downstream regulatory obligations, production sharing agreements, or energy-project law in MENA jurisdictions (Saudi Arabia, UAE, Kuwait, Qatar, Oman, Iraq, Egypt, Libya). Covers national oil company frameworks, concession and PSA structures, joint-venture arrangements, environmental and decommissioning obligations, LNG and pipeline regulation, and dispute-resolution in the energy sector. Triggers on oil and gas contracts MENA, PSA, energy licensing KSA/UAE, upstream/downstream regulation, Saudi Aramco, ADNOC, or energy project disputes.

oimiragieo Bundle

Check voice message pipeline config — verify Whisper, ElevenLabs/OpenAI TTS keys and dependencies.

sboghossian-mini-claude-for-legal Skill

Use when running the automated daily evaluation suite that measures the legal AI system's output quality across all benchmark datasets. Orchestrates the full eval pipeline — loading datasets, calling the production model, scoring with LLM-as-judge rubrics, detecting regressions, and publishing results to the leaderboard and observability dashboards.

gptomics Bundle

End-to-end 16S/ITS amplicon workflow from demultiplexed FASTQ to a consensus differential-abundance result, orchestrating cutadapt primer removal, per-run DADA2 ASV inference (learnErrors/mergeSequenceTables/removeBimeraDenovo), region-matched taxonomy assignment, a SEPP/Greengenes2 tree, alpha/beta diversity at a declared sampling depth (phyloseq/vegan, adonis2 paired with betadisper), compositional DA as a consensus of >=2 tools (ALDEx2/ANCOM-BC2) on unrarefied counts, and optional PICRUSt2 functional prediction gated on NSTI. Covers the stage-ordering decisions (primers before truncation, per-run error model, rarefy for diversity not DA, predicted potential not activity) and defers each per-step choice to the six microbiome skills. Use when staging an amplicon study end to end or chaining ASV inference, taxonomy, diversity, and differential abundance. For shotgun reads see workflows/metagenomics-pipeline.

sboghossian-mini-claude-for-legal Skill

Use to select the minimal toolset required to fulfill a request. Defaults to no tools and adds tools only when there is a clear, specific reason — preventing unnecessary RAG retrieval, web search, or paid API calls that add latency and cost without improving response quality. Consumes the output of the skip-RAG gate, tier-awareness gate, and complexity grader to produce a final tools array for the response pipeline.

oimiragieo Bundle

Implement Kubernetes security policies including NetworkPolicy, PodSecurityPolicy, and RBAC for production-grade security. Use when securing Kubernetes clusters, implementing network isolation, or enforcing pod security standards.

gptomics Bundle

Aggregates per-tool QC metrics (FastQC, fastp, alignment, quantification, variant calling, single-cell) into one interactive MultiQC report, and guides module scoping, sample-name resolution, large-cohort behavior, and turning the report into an actual QC gate. Use when summarizing QC across many samples, building a shareable quality report, or wiring automated QC into a pipeline.

oimiragieo Bundle

Design, organize, and manage Helm charts for templating and packaging Kubernetes applications with reusable configurations. Use when creating Helm charts, packaging Kubernetes applications, or implementing templated deployments.

oimiragieo Bundle

Create production-ready Kubernetes manifests for Deployments, Services, ConfigMaps, and Secrets following best practices and security standards. Use when generating Kubernetes YAML manifests, creating K8s resources, or implementing production-grade Kubernetes configurations.

oimiragieo Bundle

Improve router-facing pipeline and reflection narration to reduce noisy status churn and make Step 0/Reflection outcomes explicit. Use when updating Router output contract, reflection reminder wording, or post-pipeline notification batching.

sboghossian-mini-claude-for-legal Skill

Use to detect the deployment surface (web, mobile, voice, API, Word plugin, email) and apply appropriate output shaping rules — word limits, formatting style, citation placement, and structure depth. Runs in every response pipeline before the response is composed. Ensures that a mobile user does not receive a wall of markdown, a voice user does not receive bulleted lists, and an API caller does not receive narrative text when JSON was expected.

oimiragieo Bundle

Uses GitHub Actions or GitLab CI for CI/CD implementation.

intent-solutions-io Bundle

Transform forecasting experiments into Airflow/Prefect pipelines with monitoring. Use when deploying forecasts to production. Trigger with 'generate pipeline' or 'create Airflow DAG'.

intent-solutions-io Bundle

Generate production-ready TimeGPT forecasting pipeline code from requirements. Use when scaffolding a pipeline with validation, logging, visualization, and repeatable runs. Trigger with "create TimeGPT pipeline", "build TimeGPT integration", or "generate forecast code".

gptomics Bundle

End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundance, and function. For resistome see metagenomics/amr-detection; for strains see metagenomics/strain-tracking; for assembly see genome-assembly/metagenome-assembly.

intent-solutions-io Bundle

Produces verified datasets, verified evaluation results, and a deployable contract bundle for a workflow. Use when you need provable correctness at data and evaluation boundaries. Trigger with 'verify workflow', 'validate contract', or 'run verification pipeline'.

sboghossian-mini-claude-for-legal Skill

Use when a legal-AI platform engineer or operator needs to manage Cloudflare infrastructure — DNS records, Pages deployments, Workers scripts, R2 object storage, and KV namespaces — from within an AI-assisted workflow. Scoped to platform operations for legal-tech products; not a general Cloudflare tutorial. Triggers on requests to deploy, configure, or inspect Cloudflare resources for the legal-AI product stack.

intent-solutions-io Skill

This skill enables Claude to orchestrate complex test workflows using the test-orchestrator plugin. It allows Claude to define test execution graphs with dependencies, execute tests in parallel, and intelligently select tests to run based on code changes. Use this skill when a user requests test orchestration, dependency management for tests, parallel test execution, smart test selection, or CI/CD integration for testing. Trigger terms include "orchestrate tests", "test workflow", "parallel testing", "smart test selection", "test dependencies", and "/orchestrate".

gptomics Bundle

End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate Pearson, CEGv2 PR-AUC, copy-number artifact), method-appropriate hit calling across MAGeCK RRA/MLE, BAGEL2, drugZ, JACKS, and Chronos, cancer-cell-line copy-number correction (CRISPRcleanR / Chronos), batch correction for multi-batch screens, and the specialized branches for combinatorial paralog screens, single-cell Perturb-seq, base-editor variant-function screens, prime-editor screens, and in vivo bottleneck-aware screens. Use when analyzing any pooled CRISPR screen end-to-end, matching the hit-calling method to the experimental design, integrating copy-number correction into the pipeline, or branching the workflow for single-cell, combinatorial, base-editor, prime-editor, or in vivo variants.

intent-solutions-io Skill

This skill enables Claude to analyze and optimize cloud costs. It identifies areas for potential savings, generates cost reports, and suggests configuration changes to reduce expenses. Use this skill when the user asks to "optimize cloud costs", "reduce cloud spending", "generate a cost report", or similar requests related to cloud resource expenses. It is especially useful when the user provides details about their cloud environment (e.g., AWS, Azure, GCP). The skill leverages best practices for cost optimization and provides production-ready configurations.