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

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

Iwc Map Over Lifecycle Surveyrelated 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 Surveyrelated note— Corpus survey of Galaxy workflow recipes that turn upstream data, metadata, or small files into runtime parameters.

Nextflow workflow I/O semanticsrelated 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 schemarelated 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 schemarelated note— JSON Schema (Draft-07) validating nf-core subworkflow meta.yml — channel IO, components dependencies, authors. Upstream from nf-core/modules.