pipeline-wgbs SKILL.md skillA
pipeline-wgbs from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/pipeline-wgbs@git:20260920.6050003Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
skills/pipeline-wgbs/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 24,776 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Execute ENCODE Whole Genome Bisulfite Sequencing (WGBS) pipeline from FASTQ to methylation calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing WGBS/bisulfite-seq data, calling methylation levels, generating bedMethyl files. Trigger on: WGBS pipeline, bisulfite sequencing, methylation calling, DNA methylation pipeline, bismark, bwa-meth, bedMethyl.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# ENCODE WGBS Pipeline: FASTQ to Methylation Calls
## When to Use
- User wants to run a WGBS/bisulfite sequencing pipeline from FASTQ to methylation calls
- User asks about "WGBS pipeline", "bisulfite sequencing", "methylation calling", "Bismark", or "bedMethyl"
- User needs to process whole-genome bisulfite sequencing data following ENCODE standards
- Example queries: "process my WGBS FASTQs", "call methylation levels from bisulfite-seq", "run Bismark on my WGBS data"
Execute the ENCODE DNA methylation pipeline for Whole Genome Bisulfite Sequencing data,
producing per-CpG methylation levels in bedMethyl format.
## Pipeline Overview
```
FASTQ -> Trim adapters -> Bismark align -> Deduplicate -> sort + index -> MethylDackel -> bedMethyl
| | | | | | |
FastQC Trim Galore Bismark (Bowtie2) deduplicate_ samtools mbias + coverage
bismark extract stats
```
Paired-end only: `TRIM_GALORE` and `BISMARK_ALIGN` both take two mates, and `--reads` must
match pairs.
### ENCODE Repository
…Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-wgbs@sha256:c562390c530c1b82The line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_45z7oz7fywtgmnuj)
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Versions
The registry has recorded 5 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 48 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 24,776 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 22,864 B | A | view · diff |
| git:20260920.e127735 | 2026-09-20 | e127735 | 14,941 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 14,232 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 14,235 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 (24776 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 · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_45z7oz7fywtgmnuj GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-wgbs GET https://markdownregistry.com/api/v1/blob/c562390c530c1b82e2a5f21b654fb58f64513c30c1a94728574b5beb6b47aa07
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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