nextflow
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.
70
86%
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Medium
Suggest reviewing before use
Security
1 medium severity finding. This skill can be installed but you should review these findings before use.
W013: Attempt to modify system services in skill instructions.
What this means
The skill prompts the agent to compromise the security or integrity of the user’s machine by modifying system-level services or configurations, such as obtaining elevated privileges, altering startup scripts, or changing system-wide settings.
Why it was flagged
The skill explicitly instructs using "sudo mv nextflow /usr/local/bin/" which asks the agent/user to obtain elevated (sudo) privileges to modify a system directory, risking compromise of the machine state.
Low
Low-risk findings.
1 low severity finding. Worth noting, but not necessarily harmful.
W012: Unverifiable external dependency detected (runtime URL that controls agent).
What this means
The skill fetches instructions or code from an external URL at runtime, and the fetched content directly controls the agent’s prompts or executes code. This dynamic dependency allows the external source to modify the agent’s behavior without any changes to the skill itself.
Why it was flagged
The skill instructs users to fetch-and-execute remote installer scripts via curl piped to bash (curl -s https://get.nextflow.io | bash in SKILL.md and curl -fsSL https://get.nf-test.com | bash in references/testing.md), which downloads and runs remote code during setup.
- Repository
- K-Dense-AI/scientific-agent-skills
- Commit
757b63b
- Audited
- Security analysis
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