「mandatory」の検索結果

Bulk JIRA ops (10+ issues): transition/assign/priority/clone/delete via jira-as; dry-run mandatory. NOT single-issue ops (mk:jira-issue, mk:jira-lifecycle).

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。

Bulk Confluence ops (10+ pages): bulk-label/move/delete via confluence-as; dry-run mandatory. NOT single-page (mk:confluence-page) or comments/attachments (mk:confluence-collaborate).

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。

Use when analyzing harness trace logs to surface recurring failure patterns and suggest harness improvements. Scatter-gather pattern across last N runs with mandatory HITL gate before any change is applied. Triggers on /mk:trace-analyze, "analyze traces", "find patterns in harness runs", or after a model upgrade flagged dead-weight-audit-needed.

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。

Pre-ticket Fibonacci sizing for a paste-mode batch of user stories. Default mode is advisory-only (writes a Story Sizing Report). Opt-in `--auto-create` delegates ticket creation to mk:jira-issue + mk:jira-collaborate with mandatory dry-run + single batch confirmation gate. NOT for single-ticket estimation (mk:jira-estimator); NOT for sprint capacity (mk:planning-engine).

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。

Bulk JIRA operations on 10+ issues via the jira-as wrapper: bulk transition / assign / set-priority / clone / delete. Dry-run is MANDATORY first. Triggers: 'bulk update N issues', 'mass transition', 'transition 50+ issues to Done', 'bulk-clone', 'bulk-delete'. NOT for single-issue ops (mk:jira-issue / mk:jira-lifecycle).

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。

Bulk Confluence operations on 10+ pages via the confluence-as wrapper: bulk-label / bulk-move / bulk-delete. Dry-run is MANDATORY first. Triggers: 'bulk update N pages', 'mass label', 'delete all pages matching CQL', 'bulk-move pages to PARENT'. NOT for single-page ops (mk:confluence-page); NOT for comment/attachment ops (mk:confluence-collaborate).

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。

Publication-quality statistical visualization with mandatory best practices. Use when creating plots, charts, figures, or any data visualization. Enforces accessibility, uncertainty display, proper labeling, and statistical accuracy.

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。

Apply when creating, modifying, or reviewing any Rembric agent plugin. Triggers on changes under `apps/plugin/`, on new clients added alongside Claude Code / Codex CLI / Hermes Agent / opencode / Pi, on edits to `apps/plugin/mcp-bridge/`, `apps/plugin/bin/rembric-plugin-core.mjs`, per-client manifest changes, or plugin install/uninstall scripts. End-to-end validation against a local dev server (`pnpm run dev`, host Next.js on :3000) is mandatory whenever local testing is feasible.

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。

Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; DELFI is a method, not a package. Use when deriving fragment-based signal from cfDNA, choosing a feature family for detection vs subtyping, or diagnosing why a fragmentomic model failed validation.

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。

Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage-fitness modelling (multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data and Nextclade dataset version pinning (mandatory; lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme churn (V3/V4/V4.1/V5.3.2/Midnight) with dropout regions, and recombinant X-prefix designation lag. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater into lineage frequencies with Freyja, tracking lineage frequencies over time, handling ARTIC primer dropouts, or running surveillance for SARS-CoV-2/influenza/Mpox/RSV/H5N1/measles.

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。

Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST normCytof, premessa), and reference-anchor cross-batch normalization (CytoNorm, per-cluster quantile splines). Covers the distinction between within-run drift correction and between-batch correction, the mandatory anchor/reference sample, why normalization is per-cluster with many quantiles, and the over-correction risk. Use when correcting CyTOF signal drift, harmonizing multi-batch or multi-site studies, or deciding whether to normalize data versus model batch in the design.

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。

Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling design) using LFMM2 with mandatory K via sNMF cross-entropy elbow (LEA 3), BayPass Core/AUX/C2/IS with Omega covariance matrix, RDA / pRDA for polygenic adaptation (Forester 2018; requires imputed genotypes), OutFLANK with trimmed FST null, pcadapt, gradient forests (Ellis-Smith-Pitcher 2012, NOT mis-cited Ellis-Manel), Capblancq & Forester 2021 RDA Swiss-army-knife, genomic-offset prediction with Lind & Lotterhos 2025 three-regime caveat, Lotterhos-Whitlock sampling optima, Wang & Bradburd 2014 IBD vs IBE, and Circuitscape + ResistanceGA. Use when identifying adaptive loci across gradients, choosing K for LFMM2, deciding among GEA methods, predicting maladaptation with the novel-environment caveat, distinguishing IBD vs IBE, or optimizing sampling design.

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。

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller. Distinguishes de novo CALLING (scanning a panel for unknown variants, bounded by per-locus error and multiple testing) from tumor-informed DETECTION (tracking a pre-specified variant set, where panel integration reaches single-ppm). Covers VarDict and Mutect2 for de novo calling, UMI-aware callers, and a pysam-based known-variant VAF tracker, with matched-WBC subtraction as the mandatory defense against clonal hematopoiesis (the dominant false positive). Use when calling or tracking tumor mutations from plasma cfDNA, setting a VAF threshold, or deciding whether a low-VAF call is tumor versus CHIP.

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。

Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness via Chao1/ACE/jackknife as a lower bound, Baselga turnover/nestedness partition with the Podani alternative as sensitivity check, mandatory Hellinger transformation before ordination (Legendre & Gallagher 2001), Faith PD and SES_MPD/SES_MNTD with explicit null-model choice, and Maire 2015 functional-diversity dimensionality optimization. Use when comparing diversity across sites with unequal sampling effort, picking the right richness estimator for singleton-heavy amplicon data, partitioning beta diversity into turnover vs nestedness, reporting Hill-number effective species counts rather than raw entropies, computing SES_MPD with explicit null-model justification, or deciding whether to apply standard metrics to compositional amplicon data. Not for clinical 16S microbiome diversity (see microbiome/diversity-analysis).

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。

Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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。

Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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。

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

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。

Workflow track for tasks that need no TDD — documentation edits, governance count bumps, vendored-skill content updates, configuration tweaks, formatting, typo fixes, dependency bumps where no project code changes. Skips `/scenario` and `/implement` (no failing test to drive) and runs the work directly. `archive`, `memory-sync`, `/grant-commit`, and `/commit` remain mandatory. `verify`, `simplify`, `integrate`, and `document` are conditional — required when the diff hits one of the listed triggers, optional otherwise. `verify` is skipped only when the diff is pure-docs/prose AND `project.json → test.kind` is `behavior` (absent/invalid `test.kind` → `structural` → verify runs). Chore is a stripped-down pipeline, not a bypass; never silently skip a conditional phase whose triggers apply.

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。

MANDATORY skill for ALL code generation. Enforces top-down composition, consistent abstraction layers, and proper module hierarchy. Apply every time you write or modify code — in any language — no exceptions.

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。

Mandatory skills, conventions, and behavioral rules for Avalonia UI development using the Zafiro toolkit.

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。

Core skill activation protocol - establishes mandatory workflows for finding and applying skills before any task

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。

Implement and finalize one ready rolling-wave slice in one invocation while preserving the lifecycle boundary between implementation and independent review. Use when the user wants a slice delivered end to end without manually invoking implement-slice and finalize-slice, wants main-local implementation by default with workers only when delegation pays, followed by mandatory fresh-context finalization, or says deliver, implement and finalize, or take the slice through 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。

Use when editing AGENTS.md (package root) or templates/AGENTS.md (consumer) — enforces Thin-Root contract: hard char ceilings, ≥40% pointer ratio, mandatory emergency-triage block.

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。

Phase 4 Turn 1 of disease-market-sizing-orchestration. Generates report HTML with mandatory citation anchors per fact claim. Reads contract + staging + sources/. Every drug/treatment/stat/recommendation MUST carry [pmid:.../guideline:.../nct:...] anchor that resolves to an actual file in sources/. NEVER hardcode drug names or numerical claims. Use AFTER evidence recall (phase 3), BEFORE content-verification-layer (Turn 2).

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。