「provenance」の検索結果

Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry escalation, and conda/container software deployment on HPC and cloud. Use when deciding rule-based (Snakemake) vs channel/dataflow (Nextflow) authoring; wiring rules by OUTPUT-file pattern rather than imperative order; using wildcards + expand() for sample fan-out and constraining them to stop silent mis-routing; adding checkpoints when the set of outputs is unknown until a step runs (dynamic DAG); diagnosing why a job reran (or did not) under the mtime-plus-provenance trigger set; escalating memory on retry for OOM-killed jobs; and porting a Snakemake 7 `--cluster`/remote-provider command to the Snakemake 8+ executor-plugin and storage-plugin model (snakemake-executor-plugin-slurm) with `--software-deployment-method`.

日本語の概要は準備中です。原文の説明を表示しています。

Literature: retrieve document-level scientific evidence from publications, clinical-trial registries, and patent sources. Use for PubMed records, reproducible searches, trial registrations, patent evidence, abstracts, study metadata, stable identifiers, and citation provenance.

日本語の概要は準備中です。原文の説明を表示しています。

差分が「その差分自身を審査するレビュー基準・品質ゲート」を弱めていないかを diff-time で検出する。Check 1 レビュールールの削除・弱体化（.river/rules.md / .river/rules.d/*）、Check 2 実行時コンフィグの閾値・ゲート緩和（.river-review.{json,yaml,yml} の review.severity 引き下げ / exclude 拡大 / memory.suppressionEnabled 無効化 / selection.skills.exclude 追加）、Check 3 suppression entry の新規追加、Check 4 lint・静的解析設定からのルール削除や無効化、Check 5 branch protection・required check の緩和、の 5 Check を対象とし、これらが機能変更と同一 PR に混在し、かつ意図の宣言が無い場合に指摘する。report-only。workflow の permissions / action pin は gha-workflow-security、既存 suppression entry の使い分けは suppression-feedback、設定ファイルの一般的妥当性は config-json、.only / .skip / @ts-ignore / @ts-nocheck は heuristic-review.mjs の決定論検出器、リファクタと機能追加の混在は behavior-structure-separation へ委譲する

Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.

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Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

日本語の概要は準備中です。原文の説明を表示しています。

Port one complete feature family with provenance, current-API adaptation, repository ownership, localization, resources, and verification.

日本語の概要は準備中です。原文の説明を表示しています。

Audit project and global memory for bloat, stale decisions, duplicates, contradictions, unsafe content, missing provenance, broken routing, and over-budget global files. Load when the user asks to audit memory, clean memory, check memory health, or verify memory quality.

日本語の概要は準備中です。原文の説明を表示しています。

Compress bloated project or global memory while preserving decisions, rationale, revisit triggers, provenance, and active user preferences. Load when memory exceeds budget, global memory is too large, session logs are repetitive, or before appending to an over-budget memory file.

日本語の概要は準備中です。原文の説明を表示しています。

Loads, converts, and manipulates Hi-C contact matrices in cooler format (.cool/.mcool/.scool) and Juicer .hic, using cooler (Python + CLI), hic2cool, and hictk. Covers the single-resolution mcool URI (file.mcool::/resolutions/<bp>), the load-bearing divisive-vs-multiplicative weight-naming rule (KR/VC/VC_SQRT auto-divisive vs cooler's multiplicative weight), what survives .hic<->.cool conversion (FRAG matrices and norm vectors do not), raw-vs-balanced coarsening, the .pairs upper-triangle/chromsize-order contract, and chrom-naming/bin-table provenance. Use when loading a cooler, converting .hic to .mcool, selecting a resolution, building a cooler from pairs or a matrix, coarsening/zoomifying, importing Juicer norm vectors, or debugging all-NaN balanced matrices and chr1-vs-1 empty fetches.

日本語の概要は準備中です。原文の説明を表示しています。

Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-in-or-out-of-CDS convention, and the chr1-vs-1 seqid and gene-ID-version mismatches that silently produce all-zero count matrices and dropped joins. Use when extracting features or sequences from an annotation, converting GTF<->GFF3 or GTF->BED, traversing the gene tree, or diagnosing a coordinate/provenance mismatch upstream of counting or DE.

日本語の概要は準備中です。原文の説明を表示しています。

Build a compact Coval test set from product requirements, observed conversation failures or a coverage gap. Design realistic scenarios with separate expected behaviors, provenance and controlled voice/persona variation.

日本語の概要は準備中です。原文の説明を表示しています。

Verify supply chain integrity for AI agent plugins, tools, and dependencies. Use this skill when: - Generating SHA-256 integrity manifests for agent plugins or tool packages - Verifying that installed plugins match their published manifests - Detecting tampered, modified, or untracked files in agent tool directories - Auditing dependency pinning and version policies for agent components - Building provenance chains for agent plugin promotion (dev → staging → production) - Any request like "verify plugin integrity", "generate manifest", "check supply chain", or "sign this plugin"

日本語の概要は準備中です。原文の説明を表示しています。

Run a non-destructive open-source, npm, or public release readiness checklist covering package metadata, provenance, license, internal artifact exposure, and dry-run evidence; complements security, shipping, and sanitizer reviews, and must not publish, delete, rewrite history, or mutate release state.

日本語の概要は準備中です。原文の説明を表示しています。

Analyze source data, tables, CSV/XLSX extracts, metrics, or experiment results with explicit data-authenticity checks. Use for profiling, cleaning assumptions, statistical summaries, segmentation, trend analysis, or "analyze this data"; do not use for spreadsheet file surgery, chart design only, database migrations, or claims without data provenance.

日本語の概要は準備中です。原文の説明を表示しています。

Produces build artifacts with Software Bill of Materials (SBOM) and supply chain metadata for security and compliance. Use for "artifact publishing", "SBOM generation", "supply chain security", or "build provenance".

日本語の概要は準備中です。原文の説明を表示しています。

Designs, reconciles, and reviews an end-to-end Drydock program for safely staging agent runtimes: immutable worktree provenance, disposable VM containment, typed effect brokerage, global body accounting, resurrection, subscription-capacity economics, context compaction, operator control, evidence, and promotion. Use when several Drydock contracts must compose into one architecture, implementation hypertree, diagram set, or release plan. NOT for launching Port Daddy, running an untrusted subject, replacing focused containment/resurrection/capacity audits, or treating a design packet as runtime authority.

日本語の概要は準備中です。原文の説明を表示しています。

Secure the path from an inbound event (webhook, email, SMS, GitHub comment, file, cron) to an agent spawn in the Port Daddy fleet. Use when wiring trigger sources to agents, reviewing the io-wiring registry, adding a trust/permission gate, hardening output sinks (SSRF/path traversal), scoping tools by provenance, or proving the spawn path is safe against prompt-injection → tool-abuse. Encodes ADR-0093 and the red-team threat model. NOT for generic Coast Guard sandboxing (ADR-0050), the macaroon push-grant gate alone (ADR-0053), or non-fleet code.

日本語の概要は準備中です。原文の説明を表示しています。

Refute-before-prove research discipline: automated counterexample sweeps before any formalization, meter-integrity audits for information-bound experiments, mutation-tested model checkers, pre-registered commit-or-cut gates for speculative directions, wrong-turn reporting, and numeric-claim provenance. Use when validating any new theorem, bound, equilibrium, or security claim; when building or trusting a checker, simulator, or experiment; or when deciding whether a speculative research direction lives or dies. NOT for exploratory brainstorming, product prioritization, writing style, or literature review.

日本語の概要は準備中です。原文の説明を表示しています。

Design a normalized, machine-readable "work receipt" that answers what changed, why, by whom, and with what validation, for any AI-coding-agent task regardless of backend (Claude Code, Codex, Cursor, Aider, CI, or homegrown). Use when defining a receipt schema, normalizing heterogeneous agent logs into one evidence shape, gating PR merges on artifact-backed proof, or designing an OSS maintainer's fast-reject/fast-merge workflow. NOT for validating a DAG node's output against its own schema (use output-contract-enforcer), continuous runtime monitoring of a live coordination daemon (use runtime-verification-for-agents), or general Port Daddy claims/notes/salvage mechanics (use port-daddy-agent-skill).

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Set up @changesets/cli for semantic versioning, CHANGELOG generation, and npm publishing in a monorepo or single package. Covers init, config, contributor workflow, GitHub Actions release automation, and npm provenance.

日本語の概要は準備中です。原文の説明を表示しています。