nextflow-workflow-engine SKILL.md skillB
nextflow-workflow-engine from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/nextflow-workflow-engine@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- B, 16 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/scientific-computing/nextflow-workflow-engine/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 14,351 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure), or Kubernetes via a single config change. Powers nf-core. Use Snakemake for rule-based Python workflows; use Nextflow for containerized, cloud-native, and nf-core pipelines.
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
# Nextflow — Scalable Scientific Workflow Engine ## Overview Nextflow implements a dataflow programming model where **processes** (containerized execution units) consume and emit data through **channels** (asynchronous queues). This design enables implicit parallelization — processes run as soon as their input channels have data, without manual dependency management. Nextflow handles process orchestration across local machines, HPC clusters (SLURM, SGE, PBS), and cloud platforms (AWS Batch, Google Cloud Life Sciences, Azure Batch) by swapping a single configuration profile. The nf-core community provides 100+ validated Nextflow pipelines (RNA-seq, WGS, ChIP-seq, scRNA-seq) following best practices with automated testing. ## When to Use - Building containerized bioinformatics pipelines that must run on HPC, AWS, and local environments without code changes - Using nf-core community pipelines (nf-core/rnaseq, nf-core/sarek, nf-core/chipseq) out of the box - Processing thousands of samples with implicit parallelization across a SLURM cluster - Writing pipelines where each step runs inside a Docker or Singularity container for reproducibility …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/nextflow-workflow-engine@sha256:09823fd43c26d218The line at the top of this page pins the label git:20260428.81ea2d2, 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_mtfrdbiqd2l5adls)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 34 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 14,351 B | B | view · diff |
| git:20260414.65bebbb | 2026-04-14 | 65bebbb | 14,469 B | B | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 14,142 B | B | view |
Audit of the latest version
- fail: No curl or wget piped into a shell (matched: curl -s https://get.nextflow.io | bash)
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (14351 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 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
Starting a new one? Use a template for SKILL.md on mdpantry, which passes every one of these checks and says what to change in it.
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_mtfrdbiqd2l5adls GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/nextflow-workflow-engine GET https://markdownregistry.com/api/v1/blob/09823fd43c26d218adcc4c25ca8ee3da049a55ca664ddd52e36c351d4c97fc79
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
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.