Agent Skills Directory

Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.

Atlassian Confluence expert for creating and managing spaces, knowledge bases, and documentation. Configures space permissions and hierarchies, creates page templates with macros, sets up documentation taxonomies, designs page layouts, and manages content governance. Use when users need to build or restructure a Confluence space, design page hierarchies with permission structures, author or standardise documentation templates, embed Jira reports in pages, run knowledge base audits, or establish documentation standards and collaborative workflows.

Atlassian Template and Files Creator/Modifier expert for creating, modifying, and managing Jira and Confluence templates, blueprints, custom layouts, reusable components, and standardized content structures. Use when building org-wide templates, custom blueprints, page layouts, and automated content generation.

Atlassian Administrator for managing and organizing Atlassian products (Jira, Confluence, Bitbucket, Trello), users, permissions, security, integrations, system configuration, and org-wide governance. Use when asked to add users to Jira, change Confluence permissions, configure access control, update admin settings, manage Atlassian groups, set up SSO, install marketplace apps, review security policies, or handle any org-wide Atlassian administration task.

Cascades strategy from boardroom to individual contributor. Detects and fixes misalignment between company goals and team execution. Covers strategy articulation, cascade mapping, orphan goal detection, silo identification, communication gap analysis, and realignment protocols. Use when teams are pulling in different directions, OKRs don't connect, departments optimize locally at company expense, or when user mentions alignment, strategy cascade, silo, conflicting OKRs, or strategy communication.

Cross-functional organizational health check combining signals from all C-suite roles. Scores 8 dimensions on a traffic-light scale with drill-down recommendations. Use when assessing overall company health, preparing for board reviews, identifying at-risk functions, or when user mentions org health, health check, or health dashboard.

M&A strategy for acquiring companies or being acquired. Due diligence, valuation, integration, and deal structure. Use when evaluating acquisitions, preparing for acquisition, M&A due diligence, integration planning, or deal negotiation.

/em -hard-call — Framework for Decisions With No Good Options

Adversarial thinking partner for founders and executives. Stress-tests plans, prepares for brutal board meetings, dissects decisions with no good options, and forces honest post-mortems. Use when you need someone to find the holes before the board does, make a decision you've been avoiding, or understand what actually went wrong.

Founder onboarding interview that captures company context across 7 dimensions. Invoke with /cs:setup for initial interview or /cs:update for quarterly refresh. Generates ~/.claude/company-context.md used by all C-suite advisor skills.