nextflow
3 findings (2 critical, 1 medium), mainly command injection. Most recent scan 2026-10-21.
Second scanner: NVIDIA SkillSpector
Independent static run, no language model, over the same files as the Cisco scan above. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
Builds, runs, and debugs Nextflow DSL2 pipelines and nf-core workflows. Use for Nextflow, nf-core, .nf files, nextflow.config, processes/channels/operators, samplesheets, nf-test, modules/subworkflows, container and executor configuration, HPC/SLURM or cloud deployment, and failed or resumed pipeline runs.
- Package
- 8 files, 91 KB
- SKILL.md
- 1831 words, 12+ sections
- Code
- None. Instructions only.
- License
- Apache-2.0
- Compatibility
- Requires Bash 3.2+, Java 17-26 and Nextflow. nf-core tools requires Python 3.10+. Containers, scheduler access and network or service credentials depend on the selected workflow.
SKILL.md covers: Nextflow · Overview · When to Use This Skill · Setup · Install Nextflow (self-installing launcher) · Review the installer before executing it. · Alternative (illustrative; confirm package availability and Java compatibility) · nf-core tools (Python) for creating/linting/running nf-core assets · Two Modes of Work · Quick Start · Run an nf-core pipeline · 1. Confirm setup works (downloads pipeline + tiny test data)
Findings
CRITICAL Remote fetch followed by execution Command Injectionpipeline
Content is downloaded from the network and subsequently executed. This is a classic remote code execution attack pattern.
SKILL.md:31
# Install Nextflow (self-installing launcher)
export NXF_VER=26.04.6
curl -fsSL https://get.nextflow.io -o install-nextflow.sh
# Review the installer before executing it.
bash < install-nextflow.sh
mkdir -p "$HOME/.local/bin"
mv nextflow "$HOME/.local/bin/"
export PATH="$HOME/.local/bin:$PATH"
nextfCRITICAL Remote fetch followed by execution Command Injectionpipeline
Content is downloaded from the network and subsequently executed. This is a classic remote code execution attack pattern.
SKILL.md:43
# Install Nextflow (self-installing launcher)
export NXF_VER=26.04.6
curl -fsSL https://get.nextflow.io -o install-nextflow.sh
# Review the installer before executing it.
bash < install-nextflow.sh
mkdir -p "$HOME/.local/bin"
mv nextflow "$HOME/.local/bin/"
export PATH="$HOME/.local/bin:$PATH"
nextfMEDIUM Remote fetch followed by execution Command Injectionpipeline
Content is downloaded from the network and subsequently executed. This is a classic remote code execution attack pattern. (found in documentation — may be instructional)
references/testing.md:26
# Option 1: Conda
conda install -c conda-forge -c bioconda nf-test=0.9.5
# Option 2: upstream installer
curl -fsSL https://get.nf-test.com -o install-nf-test.sh
# Review the installer before executing it.
bash install-nf-test.sh 0.9.5
mkdir -p "$HOME/.local/bin"
mv nf-test "$HOME/.local/bin/"
exporWhat is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 15 KB |
references/configuration.md | doc | 13 KB |
references/containers.md | doc | 5.3 KB |
references/developing.md | doc | 17 KB |
references/language.md | doc | 18 KB |
references/nf-core-tools.md | doc | 6.8 KB |
references/running-pipelines.md | doc | 7.9 KB |
references/testing.md | doc | 9.0 KB |
External hosts referenced
docs.seqera.io nf-co.re github.com www.nf-test.com arxiv.org community-cr-prod.seqera.io depot.galaxyproject.org doi.org export.arxiv.org get.nextflow.io get.nf-test.com training.nextflow.io www.htslib.org
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Environment variables referenced
NXF_SINGULARITY_CACHEDIR TOWER_ACCESS_TOKEN NXF_CONDA_CACHEDIR NXF_HOME NXF_APPTAINER_CACHEDIR NXF_CLOUDCACHE_PATH
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-nextflow-scan.json
- Badge for your README:
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