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Nextflow Pipeline Assistant

End-to-end guidance for building, running, configuring, and debugging Nextflow and nf-core pipelines.

AutomationAdvanced★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

  • Writes and edits .nf scripts and nextflow.config using modern DSL2 patterns (processes, channels, operators, workflows, modules).
  • Assembles correct run commands for nf-core pipelines (rnaseq, sarek, …) with samplesheets, -profile combos, pinned revisions, and -resume.
  • Configures executors (local, SLURM, AWS/Google/Azure Batch, Kubernetes) and container engines (Docker, Singularity/Apptainer, Conda, Wave), plus resource labels and retry strategies.
  • Helps debug failed tasks and -resume cache misses, author nf-test suites for modules/subworkflows, and pass nf-core lint.

Who it's for

  • Bioinformaticians and researchers who need reproducible analysis pipelines.
  • Data/platform engineers authoring or maintaining nf-core-style pipelines and modules.
  • Teams scaling a laptop workflow out to HPC clusters or the cloud.

Examples

  1. "Build the command to run nf-core/rnaseq pinned to 3.14.0 with Docker, and show the samplesheet CSV format."
  2. "Add ext.args and a stub: block to this module and write nf-test snapshot tests."
  3. "Write a nextflow.config profile for SLURM with memory retry scaling based on task.attempt."

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/nextflow/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/nextflow folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/nextflow/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/nextflow ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and go to a working directory.
  2. Clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills folder: mkdir -p ~/.claude/skills
  4. Copy just this skill: cp -r scientific-agent-skills/skills/nextflow ~/.claude/skills/
  5. Prerequisites: confirm Java 17+ with java -version, then install Nextflow via curl -s https://get.nextflow.io | bash and put it on your PATH (or conda create -n nf -c bioconda -c conda-forge nextflow nf-core).
  6. Restart Claude Code and ask something like "help me run an nf-core pipeline" to trigger the skill.
View source on GitHub ↗License: MIT