Nextflow Pipeline Anatomy (DSL2)

Stub. Grown from cast contact, not pre-emptively (see issue #17).

Primary sources

Nextflow DSL2 docs: https://www.nextflow.io/docs/latest/dsl2.html
nf-core pipeline structure: https://nf-co.re/docs/contributing/pipelines
nf-core module spec: https://nf-co.re/docs/contributing/modules

Open gaps

Paragraphs land here when the runtime cast hits a pipeline shape SKILL.md does not cover. Each entry names the motivating target.

Incoming References (8)

Component Nextflow Channel Operators related note — Structured digest of Nextflow channel operators (47 entries) with cardinality and shape semantics; backs summarize-nextflow §6 edge reconciliation.

Component Nextflow Containers And Envs related note — Container URL grammar (depot, BioContainers, mulled-v2, Wave, ORAS) and conda directive resolution rules backing summarize-nextflow §5.

Iwc Map Over Lifecycle Survey related note — Survey of IWC map-over lifecycle recipes, with a Nextflow-to-Galaxy crosswalk for collection construction, cleanup, reshape, reduce, and publish phases.

Iwc Parameter Derivation Survey related note — Corpus survey of Galaxy workflow recipes that turn upstream data, metadata, or small files into runtime parameters.

Nextflow workflow I/O semantics related note — Defines Nextflow workflow inputs and outputs from docs plus observed fixture pipeline structures.

Nextflow parameter schema (nf-schema meta-schema) related note — JSON Schema (Draft 2020-12) meta-schema validating per-pipeline nextflow_schema.json files. Upstream from nextflow-io/nf-schema.

nf-core module meta.yml schema related note — JSON Schema (Draft-07) validating nf-core module meta.yml — channel IO, tools, containers, conda lockfiles. Upstream from nf-core/modules.

nf-core subworkflow meta.yml schema related note — JSON Schema (Draft-07) validating nf-core subworkflow meta.yml — channel IO, components dependencies, authors. Upstream from nf-core/modules.