Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/kdevos12/alkyl/nextflownpx skills add Kdevos12/ALKYL --skill nextflowgit clone --depth 1 https://github.com/Kdevos12/ALKYLWhat it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00046 | $0.00822 |
| Opus 5 | $0.00023 | $0.00411 |
| Sonnet 5 | $0.00009 | $0.00164 |
| Haiku 4.5 | $0.00005 | $0.00082 |
Grade C, and why
nextflow scanned grade C with 2 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Downloads and executes remote codehighSupply chain
curl | sh runs whatever the server returns today, which is not necessarily what it returned when this was reviewed.
curl -s https://get.nextflow.io | bash Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
curl -s https://get.nextflow.io | bash How it starts
The opening of the file, as written. The whole thing — 95 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Nextflow
Workflow language for scalable and reproducible computational pipelines — write once, run anywhere (local, HPC, AWS, GCP, Azure).
When to Use This Skill
- Writing or debugging Nextflow DSL2 pipelines (
.nffiles) - Composing processes into workflows with channel dataflow
- Configuring executors (SLURM, LSF, AWS Batch, Google Batch)
- Managing containers (Docker, Singularity/Apptainer, Conda) for reproducibility
- Building chemistry/bioinformatics pipelines (BLAST, aligners, RDKit, ORCA, Gaussian)
- Understanding
-resume/ cache behavior - Modularizing pipelines with
include/ module aliases
Quick Start — Minimal DSL2 Pipeline
// main.nf
params.input = 'data/*.sdf'
params.outdir = 'results'
process RUN_ORCA {
publishDir params.outdir, mode: 'copy'
container 'quay.io/biocontainers/orca:5.0.4--h2f1ea3e_0'
input:
path mol
output:
path "*.out"
script:
"""
orca ${mol}.inp > ${mol}.out
"""
}
workflow {
mols = channel.fromPath(params.input)
RUN_ORCA(mols)
}
Run it:
nextflow run main.nf -profile docker -resume
Router — What to Read
| Task | Reference |
|---|---|
| Processes, channels, input/output qualifiers, script types | references/core-concepts.md |
| Workflows, named workflows, pipe/and operators, modules, composition | references/pipeline-patterns.md |
nextflow.config, executors, profiles, HPC/cloud, cache/resume |
references/execution-config.md |
| Docker, Apptainer/Singularity, Conda, Wave, reproducibility | references/containers-envs.md |
| Channel factories, operators, file handling, remote files | references/files-channels.md |
| Chemistry/bioinformatics patterns (BLAST, RDKit, ORCA, MD) | references/chem-bioinformatics.md |
Key Concepts at a Glance
| Concept | What it is |
|---|---|
process |
Runs a script/command; defines input, output, directives |
workflow |
Composes processes and operators via dataflow channels |
channel |
Asynchronous stream of values connecting processes |
val / path |
Input qualifiers — val for data, path for staged files |
publishDir |
Copies task output to a user-visible results directory |
executor |
Where tasks run: local, slurm, awsbatch, google-batch… |
-resume |
Reuses cached task results; skips unchanged tasks |
module |
Reusable .nf file included with include { X } from './module' |
What ships with it
6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2d ago First seen · 95 lines · 46 tokens per session scan C 40d3d2d6e109
nextflow is a skill published in the GitHub repository Kdevos12/ALKYL (6 stars, last pushed 5mo ago), licensed MIT. It adds 46 tokens to every session and 822 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it C with 2 findings (downloads and executes remote code, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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