k-dense-ai/scientific-agent-skills · skills/nextflow/SKILL.md

nextflow skillB

nextflow is agent-read markdown (skill) from k-dense-ai/scientific-agent-skills: Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or deb.

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.

How to install

Latest version
mdr add k-dense-ai/scientific-agent-skills/nextflow@v1.2
Exact content
mdr add k-dense-ai/scientific-agent-skills/nextflow@sha256:4ef839f586a77e58

Pin 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.

Badge

mdr badge

[![mdr](https://markdownregistry.com/badge/art_vxnsglsq55rra6xj.svg)](https://markdownregistry.com/a/art_vxnsglsq55rra6xj)

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Versions

versioncommittedcommitsizeaudit
v1.2 latest2026-09-02 1e5eeff 13,172 BB view · diff
v1.12026-07-31 4226ca8 12,214 BB view · diff
v1.02026-07-31 bd99c01 12,214 BB view · diff
v1.02026-07-26 b085e11 12,211 BB view · diff
git:20260611.1b8fae32026-06-11 1b8fae3 12,216 BB view

Audit of the latest version

B  16 of 17 checks passed. Deterministic, no model, same answer every run.
  • 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 (13172 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

Source

GitHub

k-dense-ai/scientific-agent-skills · 43,331 stars · license MIT · pushed 2026-09-02 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_vxnsglsq55rra6xj
GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/nextflow
GET https://markdownregistry.com/api/v1/blob/4ef839f586a77e582bf25ee7c19a01aabf5d7b36c47be5cc6ce541b4e0883b05