nextflow

Editorial and source context

What this Skill does

Nextflow is a source-indexed Agent Skill for cloud, devops & infrastructure work. Based on the SKILL.md description, it focuses on build, run, and debug nextflow data pipelines and nf-core workflows end to end. Use the linked GitHub file to confirm scope and prerequisites before enabling it.

What the author says

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 debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word "Nextflow", and for authoring nf-core-compliant pipelines, modules, configs, and linting.

Compatibility and requirements

• Use an agent runtime that supports Agent Skills and the linked SKILL.md format.
• Confirm the source repository's tools, SDKs, and platform prerequisites for azure ai work.

How to install or import it

• Open the linked GitHub SKILL.md and review its scope and setup instructions.
• Install or import the skill using the agent runtime's documented workflow.
• Run a small, non-sensitive test and verify the output before broader use.

Permissions and risks

• Review every command, file path, network request, dependency, and credential scope before enabling it.
• GitHub stars indicate popularity, not safety or correctness; validate the source and test with non-sensitive data.

Example workflows

• Ask an AI agent to apply Nextflow to azure ai work described in the source record.
• Have the agent state assumptions, required tools, and expected output before using this cloud, devops & infrastructure skill.
• Compare the result with the linked GitHub SKILL.md and verify it against your project requirements.