ngs-analysis-router

# Life Sciences NGS Analysis Router Use this skill as the top-level entrypoint for ambiguous or broad sequencing-analysis requests. ## Start Here Inspect the available inputs before asking the user questions. Look for: - Illumina run-folder files: `RunInfo.xml`, `RunParameters.xml`, `SampleSheet.csv`, `Data/Intensities/BaseCalls` - FASTQs: `*.fastq`, `*.fq`, `*.fastq.gz`, `*.fq.gz` - BAM/CRAM/VCF: `*.bam`, `*.cram`, `*.vcf`, `*.vcf.gz` - count matrices: `matrix.mtx`, `features.tsv`, `barcodes.tsv`, `*.h5`, `*.h5ad`, `*.rds` - metadata: sample sheets, design files, target BEDs, reference FASTA/GTF, primer files Read `references/intake-schema.json` and `references/pipeline-registry.json` when forming the route. ## Intake Rules Ask 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. Always resolve: - input type - assay type - desired output - organism/reference - paired-end vs single-end when FASTQs are involved - any assay-specific design file or metadata required for the requested result - runtime constraints: local/HPC/cloud, container availability, and whether installs are allowed For human data, ask whether cloud upload is allowed before suggesting BaseSpace, Terra, DNAnexus, or any cloud path. ## Routing Route to one leaf skill: - BCL run folder or demultiplexing: `ngs-bcl-to-fastq` - QC/trimming only: `ngs-fastq-qc` - WGS/WES/panel variants: `ngs-dna-variant-calling`, then a subtype skill when the analysis model is clear - germline WGS/WES/panel variants: `ngs-dna-germline-variants` - tumor-normal or tumor-only somatic variants: `ngs-dna-somatic-variants` - UMI, duplex, or low-frequency targeted panels: `ngs-dna-umi-panel-variants` - bulk RNA-seq kickoff: `ngs-bulk-rnaseq` - bulk RNA-seq FASTQ-to-count QC: `ngs-bulk-rnaseq-counts-qc` - bulk RNA-seq differential expression from counts: `ngs-bulk-rnaseq-differential-expression` - single-cell or single-nucleus FASTQ-to-matrix kickoff: `ngs-scrna-seq` - single-cell or single-nucleus post-count QC/annotation/UMAP: `scrna-seq-qc` - epigenomics kickoff: `ngs-epigenomics-peaks` - ATAC-seq QC/peaks/accessibility: `ngs-atacseq-peaks-qc` - ChIP-seq, CUT&RUN, or CUT&Tag QC/peaks: `ngs-chip-cutrun-peaks-qc` - 16S/18S/ITS/COI amplicons: `ngs-amplicon-microbiome` - shotgun metagenomics: `ngs-shotgun-metagenomics` - runtime/package setup only: `ngs-runtime-env` Prefer public, runtime-installable packages and nf-core workflows. Surface license/EULA/account boundaries before using proprietary or cloud tools. ## Preflight Before proposing installation or execution, run a preflight plan from the repo root: ```bash python plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline <pipeline_key> --emit-install-plan ``` When the user needs an approval-ready install handoff, write persistent install artifacts: ```bash python plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline <pipeline_key> --manager micromamba --install-plan-outdir runtime_readiness/<pipeline_key>_install ``` Treat `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`. For reference- or database-heavy pipelines, also create a resource plan before saying the workflow is runnable: ```bash python plugins/ngs-analysis/scripts/ngs_reference_manager.py plan --pipeline <pipeline_key> --genome-build <build> --outdir resource_readiness/<pipeline_key> ``` Use `--include-optional` for shotgun, amplicon, or motif-enabled epigenomics runs when optional databases materially affect the requested output. Use `--network-checks` only when the user allows network checks. Use `--install-missing --yes` only when the user explicitly asks to install. ## Output Contract Return: 1. the routed analysis type and confidence 2. missing essential parameters, if any 3. recommended public pipeline or package family 4. local tool preflight summary 5. preflight-first command or next concrete action 6. caveats around licenses, cloud upload, database size, and reference data