pipeline-guide skillA
pipeline-guide is agent-read markdown (skill) from ammawla/encode-toolkit: Access ENCODE uniform analysis pipelines, generate user-specific Nextflow/WDL pipelines, manage compute resources, and integrate with cloud platforms. Use when the user wants to understand ENCODE pipelines, run pipelines on their own data, generate custom Nextflow workflows from ENCODE pipeline code, check compute requirements (CPU/GPU/memory), run pipelines in background, or integrate with Google Cloud, AWS, or other cloud platforms. Also use when the user asks about ENCODE pipeline outputs, pr.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
# ENCODE Pipeline Guide and Custom Workflow Generation ## When to Use - User wants to understand ENCODE uniform analysis pipelines or run them on their own data - User asks about "ENCODE pipeline", "Nextflow", "WDL", "processing standards", or "pipeline requirements" - User needs to generate a custom Nextflow/WDL workflow based on ENCODE pipeline specifications - User wants to know compute requirements (CPU, GPU, memory, storage) for running pipelines - Example queries: "how do I run the ENCODE ChIP-seq pipeline?", "what are the compute requirements for Hi-C processing?", "generate a Nextflow pipeline for my ATAC-seq data" Understand ENCODE pipelines, generate user-specific workflows in Nextflow/WDL, and manage compute resources for local, HPC, and cloud execution. ## ENCODE Uniform Analysis Pipelines ENCODE uses standardized pipelines for each assay type, ensuring reproducibility across all datasets. All pipelines are: - **Open source**: GitHub (github.com/ENCODE-DCC) - **Containerized**: Docker and Singularity images - **Written in WDL**: Workflow Description Language (Cromwell execution engine) …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-guide@git:20260921.4ba10c6mdr add ammawla/encode-toolkit/pipeline-guide@sha256:f4671821fc7a06b1Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_umx4d5fd67kfjz5o)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.4ba10c6 latest | 2026-09-21 | 4ba10c6 | 33,127 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 33,144 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 31,297 B | A | view · diff |
| git:20260920.1c6c84b | 2026-09-20 | 1c6c84b | 26,748 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 26,217 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (33127 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_umx4d5fd67kfjz5o GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-guide GET https://markdownregistry.com/api/v1/blob/f4671821fc7a06b1c4879f96cb4386ac76cc924b2adc24f7120a9fedb9780275
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