| name | nf-core-pipeline-list |
| description | Use this skill to verify the repo-managed nf-core tools install and retrieve a cleaned summary of available pipelines. Do not use it for interactive launch flows or full pipeline downloads. |
Purpose
Check that nf-core tools run correctly in the repo-local environment and return a deterministic pipeline summary.
When to use
- You need a quick nf-core installation check.
- You want a compact machine-readable view of available nf-core pipelines.
When not to use
- You need interactive parameter entry with
nf-core launch.
- You need to download or execute a full nf-core pipeline.
Inputs
- Optional
--sort and --limit
Outputs
- Cleaned JSON summary with local and remote nf-core pipeline metadata
Requirements
- The repo-local toolchain at
slurm/envs/nextflow-tools
- Network access for the remote pipeline catalog
Procedure
- Run
python3 skills/reproducible-workflows/nf-core-pipeline-list/scripts/list_nfcore_pipelines.py --limit 5.
- Inspect
counts.remote_workflows and the returned remote_workflows entries.
- Use the names and release metadata as a starting point for later nf-core workflows.
Validation
- The wrapper runs
nf-core pipelines list successfully through the repo-local environment.
- The malformed multiline JSON emitted by the CLI is cleaned and parsed.
- At least one remote pipeline is returned.
Failure modes and fixes
- JSON parse issues: use the provided wrapper instead of calling
nf-core --json directly.
- Empty remote list: check outbound network access and retry.
Safety and limits
- This skill verifies catalog access only.
- It does not prove that any specific nf-core pipeline can be executed locally.
Examples
python3 .../list_nfcore_pipelines.py --sort pulled --limit 3
Provenance
Related skills
nextflow-hello-workflowsnakemake-toy-workflow-starter
