Nf core pipeline list

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

1. Run python3 skills/reproducible-workflows/nf-core-pipeline-list/scripts/list_nfcore_pipelines.py --limit 5.
2. Inspect counts.remote_workflows and the returned remote_workflows entries.
3. 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

• nf-core tools installation docs: https://nf-co.re/docs/nf-core-tools/installation
• nf-core pipelines list docs: https://nf-co.re/docs/nf-core-tools/pipelines/list

Related skills

• nextflow-hello-workflow
• snakemake-toy-workflow-starter