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This skill can execute the plugin-owned local FastQ QC runner when the user approves a local run. It should decide whether trimming or additional investigation is warranted; it should not blindly trim by default.\n\n## Essential Inputs\n\nConfirm:\n\n- FASTQ paths and pairing convention\n- whether output should be QC-only or trimmed FASTQs\n- known adapter or primer sequences\n- organism if contamination screening or host depletion is requested\n- output directory\n- whether FASTQs are raw, demultiplexed, previously trimmed, or downloaded from an archive\n- whether downstream analysis expects original read lengths, UMIs, or inline barcodes\n\n## Public Tools\n\nDefault tool set:\n\n- `FastQC` for raw read QC\n- `MultiQC` for project-level summary\n- `fastp` for all-in-one QC\u002Ftrimming when acceptable\n- `Cutadapt` when primer\u002Fadapter handling needs explicit sequences\n- `seqkit` for quick counts, stats, and subsampling\n\n## Preflight\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Fngs_preflight.py --pipeline fastq_qc --emit-install-plan\n```\n\n## Local Execution\n\nUse the plugin-owned runner for local artifact-producing FASTQ QC:\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Frun_fastq_qc.py \\\n  --sample-sheet samplesheet.csv \\\n  --execute\n```\n\nSingle paired sample:\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Frun_fastq_qc.py \\\n  --sample sampleA \\\n  --r1 sampleA_R1.fastq.gz \\\n  --r2 sampleA_R2.fastq.gz \\\n  --execute\n```\n\nOptional trimming branch:\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Frun_fastq_qc.py \\\n  --sample-sheet samplesheet.csv \\\n  --trim-mode fastp \\\n  --execute\n```\n\nFor explicit adapters:\n\n```bash\npython plugins\u002Fngs-analysis\u002Fscripts\u002Frun_fastq_qc.py \\\n  --sample-sheet samplesheet.csv \\\n  --trim-mode cutadapt \\\n  --adapter-r1 AGATCGGAAGAGC \\\n  --adapter-r2 AGATCGGAAGAGC \\\n  --execute\n```\n\nThe runner performs pre-execution validation before Snakemake execution. It writes a timestamped run directory with `run_manifest.json`, `config.json`, `validation\u002F`, `workflow\u002FSnakefile`, logs, `artifact_index.json`, `summary.md`, FastQC\u002FMultiQC outputs, and `qc_interpretation.json` after successful execution.\n\n## Interpretation Rules\n\nInspect raw QC before recommending trimming:\n\n- Per-base quality drop at the read end: consider quality trimming, but preserve enough length for alignment or amplicon merging.\n- Adapter or primer signal: use `cutadapt` when explicit sequences matter; use `fastp` only when automatic handling is acceptable.\n- Poly-G or patterned-flowcell artifacts: handle with a tool that explicitly supports the artifact and report the assumption.\n- Overrepresented sequences: classify adapters, primers, rRNA, PhiX, host contamination, or true biology before filtering.\n- Per-tile failures or severe quality shifts: flag possible run-level issues and avoid treating them as ordinary adapter contamination.\n- High duplication: interpret by assay; it may be expected for amplicons, targeted panels, or low-input libraries.\n- Pairing issues: verify R1\u002FR2 file counts and read-name pairing before any downstream workflow.\n\nDo not overwrite input FASTQs. Preserve the raw QC reports even when trimmed FASTQs are created.\n\n## Kickoff Pattern\n\nQC-only:\n\n```bash\nmkdir -p results\u002Ffastqc results\u002Fmultiqc\nfastqc -t 4 -o results\u002Ffastqc *.fastq.gz\nmultiqc results\u002Ffastqc -o results\u002Fmultiqc\n```\n\nQC plus trimming:\n\n```bash\nfastp \\\n  -i sample_R1.fastq.gz \\\n  -I sample_R2.fastq.gz \\\n  -o results\u002Ftrimmed\u002Fsample_R1.fastq.gz \\\n  -O results\u002Ftrimmed\u002Fsample_R2.fastq.gz \\\n  --html results\u002Ffastp\u002Fsample.html \\\n  --json results\u002Ffastp\u002Fsample.json\nmultiqc results -o results\u002Fmultiqc\n```\n\n## Output Review\n\nReturn a short QC interpretation with:\n\n1. sample\u002Fread-pair inventory\n2. QC modules that look normal\n3. 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Use when the user wants Codex to create a command-line tool that can run from any repo, expose composable read\u002Fwrite commands, return stable JSON, manage auth, and pair with a companion skill.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1165,1168,1171],{"name":1166,"slug":1167,"type":15},"API Development","api-development",{"name":1169,"slug":1170,"type":15},"CLI","cli",{"name":1172,"slug":1173,"type":15},"Codex","codex","2026-04-12T05:07:04.132762",{"slug":1176,"name":1176,"fn":1177,"description":1178,"org":1179,"tags":1180,"stars":1139,"repoUrl":1140,"updatedAt":1191},"cloudflare-deploy","deploy projects to Cloudflare","Deploy applications and infrastructure to Cloudflare using Workers, Pages, and related platform services. Use when the user asks to deploy, host, publish, or set up a project on Cloudflare.",{"slug":8,"name":9,"logoUrl":10,"githubOrg":8},[1181,1184,1187,1188],{"name":1182,"slug":1183,"type":15},"Cloudflare","cloudflare",{"name":1185,"slug":1186,"type":15},"Cloudflare Pages","cloudflare-pages",{"name":1029,"slug":1030,"type":15},{"name":1189,"slug":1190,"type":15},"Deployment","deployment","2026-04-12T05:07:14.275118",{"slug":1193,"name":1193,"fn":1194,"description":1195,"org":1196,"tags":1197,"stars":1139,"repoUrl":1140,"updatedAt":1210},"define-goal","define and set measurable project goals","Help the user define a concrete, measurable goal before starting work, especially when they ask to use the goal tool, create a goal, set an objective, clarify success criteria, or turn a fuzzy intention into a quantitative outcome. 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},[1198,1201,1204,1207],{"name":1199,"slug":1200,"type":15},"Productivity","productivity",{"name":1202,"slug":1203,"type":15},"Project Management","project-management",{"name":1205,"slug":1206,"type":15},"Strategy","strategy",{"name":1208,"slug":1209,"type":15},"Task Management","task-management","2026-05-23T06:17:16.870838",{"slug":1212,"name":1212,"fn":1213,"description":1214,"org":1215,"tags":1216,"stars":1139,"repoUrl":1140,"updatedAt":1222},"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},[1217,1218,1220,1221],{"name":991,"slug":992,"type":15},{"name":1219,"slug":1212,"type":15},"Figma",{"name":1048,"slug":1049,"type":15},{"name":1155,"slug":1156,"type":15},"2026-04-12T05:06:47.939943",{"slug":1224,"name":1224,"fn":1225,"description":1226,"org":1227,"tags":1228,"stars":1139,"repoUrl":1140,"updatedAt":1236},"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},[1229,1230,1233,1234,1235],{"name":991,"slug":992,"type":15},{"name":1231,"slug":1232,"type":15},"Design System","design-system",{"name":1219,"slug":1212,"type":15},{"name":1048,"slug":1049,"type":15},{"name":1057,"slug":1058,"type":15},"2026-05-10T05:59:52.971881",{"slug":1238,"name":1238,"fn":1239,"description":1240,"org":1241,"tags":1242,"stars":1139,"repoUrl":1140,"updatedAt":1250},"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},[1243,1244,1245,1248,1249],{"name":991,"slug":992,"type":15},{"name":1231,"slug":1232,"type":15},{"name":1246,"slug":1247,"type":15},"Documentation","documentation",{"name":1219,"slug":1212,"type":15},{"name":1048,"slug":1049,"type":15},"2026-05-16T06:07:47.821474",{"slug":1252,"name":1252,"fn":1253,"description":1254,"org":1255,"tags":1256,"stars":1139,"repoUrl":1140,"updatedAt":1262},"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},[1257,1258,1259,1260,1261],{"name":991,"slug":992,"type":15},{"name":1219,"slug":1212,"type":15},{"name":1048,"slug":1049,"type":15},{"name":1057,"slug":1058,"type":15},{"name":1137,"slug":1138,"type":15},"2026-05-16T06:07:40.583615",{"slug":1264,"name":1264,"fn":1265,"description":1266,"org":1267,"tags":1268,"stars":1139,"repoUrl":1140,"updatedAt":1277},"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},[1269,1272,1273,1276],{"name":1270,"slug":1271,"type":15},"Animation","animation",{"name":1172,"slug":1173,"type":15},{"name":1274,"slug":1275,"type":15},"Creative","creative",{"name":991,"slug":992,"type":15},"2026-05-02T05:31:48.48485",{"slug":1279,"name":1279,"fn":1280,"description":1281,"org":1282,"tags":1283,"stars":1139,"repoUrl":1140,"updatedAt":1293},"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},[1284,1285,1286,1289,1292],{"name":1274,"slug":1275,"type":15},{"name":991,"slug":992,"type":15},{"name":1287,"slug":1288,"type":15},"Image Generation","image-generation",{"name":1290,"slug":1291,"type":15},"Images","images",{"name":9,"slug":8,"type":15},"2026-05-15T06:23:24.312127",675]