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Look for:\n\n- Illumina run-folder files: `RunInfo.xml`, `RunParameters.xml`, `SampleSheet.csv`, `Data\u002FIntensities\u002FBaseCalls`\n- FASTQs: `*.fastq`, `*.fq`, `*.fastq.gz`, `*.fq.gz`\n- BAM\u002FCRAM\u002FVCF: `*.bam`, `*.cram`, `*.vcf`, `*.vcf.gz`\n- count matrices: `matrix.mtx`, `features.tsv`, `barcodes.tsv`, `*.h5`, `*.h5ad`, `*.rds`\n- metadata: sample sheets, design files, target BEDs, reference FASTA\u002FGTF, primer files\n\nRead `references\u002Fintake-schema.json` and `references\u002Fpipeline-registry.json` when forming the route.\n\n## Intake Rules\n\nAsk the smallest set of missing questions needed to choose a defensible pipeline. Do not ask the full questionnaire if file inspection already answers a field.\n\nAlways resolve:\n\n- input type\n- assay type\n- desired output\n- organism\u002Freference\n- paired-end vs single-end when FASTQs are involved\n- any assay-specific design file or metadata required for the requested result\n- runtime constraints: local\u002FHPC\u002Fcloud, container availability, and whether installs are allowed\n\nFor human data, ask whether cloud upload is allowed before suggesting BaseSpace, Terra, DNAnexus, or any cloud path.\n\n## Routing\n\nRoute to one leaf skill:\n\n- BCL run folder or demultiplexing: `ngs-bcl-to-fastq`\n- QC\u002Ftrimming only: `ngs-fastq-qc`\n- WGS\u002FWES\u002Fpanel variants: `ngs-dna-variant-calling`, then a subtype skill when the analysis model is clear\n- germline WGS\u002FWES\u002Fpanel variants: `ngs-dna-germline-variants`\n- tumor-normal or tumor-only somatic variants: `ngs-dna-somatic-variants`\n- UMI, duplex, or low-frequency targeted panels: `ngs-dna-umi-panel-variants`\n- bulk RNA-seq kickoff: `ngs-bulk-rnaseq`\n- bulk RNA-seq FASTQ-to-count QC: `ngs-bulk-rnaseq-counts-qc`\n- bulk RNA-seq differential expression from counts: `ngs-bulk-rnaseq-differential-expression`\n- single-cell or single-nucleus FASTQ-to-matrix kickoff: `ngs-scrna-seq`\n- single-cell or single-nucleus post-count QC\u002Fannotation\u002FUMAP: `scrna-seq-qc`\n- epigenomics kickoff: `ngs-epigenomics-peaks`\n- ATAC-seq QC\u002Fpeaks\u002Faccessibility: `ngs-atacseq-peaks-qc`\n- ChIP-seq, CUT&RUN, or CUT&Tag QC\u002Fpeaks: `ngs-chip-cutrun-peaks-qc`\n- 16S\u002F18S\u002FITS\u002FCOI amplicons: `ngs-amplicon-microbiome`\n- shotgun metagenomics: `ngs-shotgun-metagenomics`\n- runtime\u002Fpackage setup only: `ngs-runtime-env`\n\nPrefer public, runtime-installable packages and nf-core workflows. Surface license\u002FEULA\u002Faccount boundaries before using proprietary or cloud tools.\n\n## Preflight\n\nBefore proposing installation or execution, run a preflight plan from the repo root:\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Fngs_preflight.py --pipeline \u003Cpipeline_key> --emit-install-plan\n```\n\nWhen the user needs an approval-ready install handoff, write persistent install artifacts:\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Fngs_preflight.py --pipeline \u003Cpipeline_key> --manager micromamba --install-plan-outdir runtime_readiness\u002F\u003Cpipeline_key>_install\n```\n\nTreat `install_plan.json` as the canonical review artifact. `install_commands.sh` is generated from the same plan and stays review-only unless the user explicitly approves execution with `NGS_RUN_INSTALL_COMMANDS=1`.\n\nFor reference- or database-heavy pipelines, also create a resource plan before saying the workflow is runnable:\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Fngs_reference_manager.py plan --pipeline \u003Cpipeline_key> --genome-build \u003Cbuild> --outdir resource_readiness\u002F\u003Cpipeline_key>\n```\n\nUse `--include-optional` for shotgun, amplicon, or motif-enabled epigenomics runs when optional databases materially affect the requested output.\n\nUse `--network-checks` only when the user allows network checks. 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Use this skill for goal creation and goal refinement only; it does not manage durable snapshots, decision logs, or long-running execution artifacts.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1101,1104,1107,1110],{"name":1102,"slug":1103,"type":15},"Productivity","productivity",{"name":1105,"slug":1106,"type":15},"Project Management","project-management",{"name":1108,"slug":1109,"type":15},"Strategy","strategy",{"name":1111,"slug":1112,"type":15},"Task Management","task-management","2026-05-23T06:17:16.870838",{"slug":1115,"name":1115,"fn":1116,"description":1117,"org":1118,"tags":1119,"stars":1042,"repoUrl":1043,"updatedAt":1125},"figma","translate Figma designs into code","Use the Figma MCP server to fetch design context, screenshots, variables, and assets from Figma, and to translate Figma nodes into production code. Trigger when a task involves Figma URLs, node IDs, design-to-code implementation, or Figma MCP setup and troubleshooting.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1120,1121,1123,1124],{"name":894,"slug":895,"type":15},{"name":1122,"slug":1115,"type":15},"Figma",{"name":951,"slug":952,"type":15},{"name":1058,"slug":1059,"type":15},"2026-04-12T05:06:47.939943",{"slug":1127,"name":1127,"fn":1128,"description":1129,"org":1130,"tags":1131,"stars":1042,"repoUrl":1043,"updatedAt":1139},"figma-code-connect-components","connect Figma designs to code components","Connects Figma design components to code components using Code Connect mapping tools. Use when user says \"code connect\", \"connect this component to code\", \"map this component\", \"link component to code\", \"create code connect mapping\", or wants to establish mappings between Figma designs and code implementations. For canvas writes via `use_figma`, use `figma-use`.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1132,1133,1136,1137,1138],{"name":894,"slug":895,"type":15},{"name":1134,"slug":1135,"type":15},"Design System","design-system",{"name":1122,"slug":1115,"type":15},{"name":951,"slug":952,"type":15},{"name":960,"slug":961,"type":15},"2026-05-10T05:59:52.971881",{"slug":1141,"name":1141,"fn":1142,"description":1143,"org":1144,"tags":1145,"stars":1042,"repoUrl":1043,"updatedAt":1153},"figma-create-design-system-rules","generate design system rules from Figma","Generates custom design system rules for the user's codebase. Use when user says \"create design system rules\", \"generate rules for my project\", \"set up design rules\", \"customize design system guidelines\", or wants to establish project-specific conventions for Figma-to-code workflows. Requires Figma MCP server connection.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1146,1147,1148,1151,1152],{"name":894,"slug":895,"type":15},{"name":1134,"slug":1135,"type":15},{"name":1149,"slug":1150,"type":15},"Documentation","documentation",{"name":1122,"slug":1115,"type":15},{"name":951,"slug":952,"type":15},"2026-05-16T06:07:47.821474",{"slug":1155,"name":1155,"fn":1156,"description":1157,"org":1158,"tags":1159,"stars":1042,"repoUrl":1043,"updatedAt":1165},"figma-implement-design","translate Figma designs into application code","Translates Figma designs into production-ready application code with 1:1 visual fidelity. Use when implementing UI code from Figma files, when user mentions \"implement design\", \"generate code\", \"implement component\", provides Figma URLs, or asks to build components matching Figma specs. For Figma canvas writes via `use_figma`, use `figma-use`.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1160,1161,1162,1163,1164],{"name":894,"slug":895,"type":15},{"name":1122,"slug":1115,"type":15},{"name":951,"slug":952,"type":15},{"name":960,"slug":961,"type":15},{"name":1040,"slug":1041,"type":15},"2026-05-16T06:07:40.583615",{"slug":1167,"name":1167,"fn":1168,"description":1169,"org":1170,"tags":1171,"stars":1042,"repoUrl":1043,"updatedAt":1180},"hatch-pet","create animated pets for Codex","Create, repair, validate, visually QA, and package Codex-compatible animated pets and pet spritesheets from character art, generated images, company or prospect brand cues, or visual references. Use when a user wants a lightweight-worker Codex pet workflow, a non-pixel custom pet style, a prospect or company mascot pet, or a full 8x9 animated pet atlas with transparent unused cells, QA contact sheets, and pet.json packaging. This skill composes the installed $imagegen system skill for visual generation and uses bundled scripts for deterministic spritesheet assembly.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1172,1175,1176,1179],{"name":1173,"slug":1174,"type":15},"Animation","animation",{"name":1075,"slug":1076,"type":15},{"name":1177,"slug":1178,"type":15},"Creative","creative",{"name":894,"slug":895,"type":15},"2026-05-02T05:31:48.48485",{"slug":1182,"name":1182,"fn":1183,"description":1184,"org":1185,"tags":1186,"stars":1042,"repoUrl":1043,"updatedAt":1196},"imagegen","generate and edit raster images","Generate or edit raster images when the task benefits from AI-created bitmap visuals such as photos, illustrations, textures, sprites, mockups, or transparent-background cutouts. Use when Codex should create a brand-new image, transform an existing image, or derive visual variants from references, and the output should be a bitmap asset rather than repo-native code or vector. Do not use when the task is better handled by editing existing SVG\u002Fvector\u002Fcode-native assets, extending an established icon or logo system, or building the visual directly in HTML\u002FCSS\u002Fcanvas.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1187,1188,1189,1192,1195],{"name":1177,"slug":1178,"type":15},{"name":894,"slug":895,"type":15},{"name":1190,"slug":1191,"type":15},"Image Generation","image-generation",{"name":1193,"slug":1194,"type":15},"Images","images",{"name":9,"slug":8,"type":15},"2026-05-15T06:23:24.312127",675]