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Support Nextflow typed syntax for process inputs/outputs #4

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Merged
ewels merged 10 commits into from
Mar 3, 2026
Merged

Support Nextflow typed syntax for process inputs/outputs #4

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bfc1968
Support Nextflow typed syntax for process inputs/outputs
ewels Mar 3, 2026
66d57ab
Fix bare typed outputs and ? type from LSP hover
ewels Mar 3, 2026
f747d3b
Enrich bare typed outputs from .nf source files
ewels Mar 3, 2026
31c9d05
Fix params not showing: prefix README heading IDs to avoid collisions
ewels Mar 3, 2026
3e6b1cf
Show pattern restriction in HTML parameter cards
ewels Mar 3, 2026
f46930a
Apply Groovydoc @param/@return descriptions to process inputs/outputs
ewels Mar 3, 2026
472ad33
Add nf-fgsv as example pipeline
ewels Mar 3, 2026
3bdae14
Refactor: eliminate duplicated file reads and extract shared constants
ewels Mar 3, 2026
f931d09
Merge remote-tracking branch 'origin/main' into fix/typed-process-io-…
ewels Mar 3, 2026
91a8e99
Add YAML and Table example outputs for nf-fgsv
ewels Mar 3, 2026
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1 change: 1 addition & 0 deletions docs/examples.md
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Expand Up @@ -8,4 +8,5 @@ Generated documentation for real-world Nextflow pipelines.
| rnaseq-nf | Simple RNA-seq pipeline | [HTML](examples/rnaseq-nf/index.html) | [Markdown](examples/rnaseq-nf/markdown/index.md) | [Table](examples/rnaseq-nf/table/README.md) | [JSON](examples/rnaseq-nf/json/pipeline-api.json) | [YAML](examples/rnaseq-nf/yaml/pipeline-api.yaml) |
| rnavar | nf-core/rnavar — RNA variant calling | [HTML](examples/rnavar/index.html) | [Markdown](examples/rnavar/markdown/index.md) | [Table](examples/rnavar/table/README.md) | [JSON](examples/rnavar/json/pipeline-api.json) | [YAML](examples/rnavar/yaml/pipeline-api.yaml) |
| sarek | nf-core/sarek — variant calling & annotation | [HTML](examples/sarek/index.html) | [Markdown](examples/sarek/markdown/index.md) | [Table](examples/sarek/table/README.md) | [JSON](examples/sarek/json/pipeline-api.json) | [YAML](examples/sarek/yaml/pipeline-api.yaml) |
| nf-fgsv | Fulcrum Genomics structural variant calling | [HTML](examples/nf-fgsv/index.html) | [Markdown](examples/nf-fgsv/markdown/index.md) | [Table](examples/nf-fgsv/table/README.md) | [JSON](examples/nf-fgsv/json/pipeline-api.json) | [YAML](examples/nf-fgsv/yaml/pipeline-api.yaml) |
| wf-metagenomics | Oxford Nanopore metagenomics workflow | [HTML](examples/wf-metagenomics/index.html) | [Markdown](examples/wf-metagenomics/markdown/index.md) | [Table](examples/wf-metagenomics/table/README.md) | [JSON](examples/wf-metagenomics/json/pipeline-api.json) | [YAML](examples/wf-metagenomics/yaml/pipeline-api.yaml) |
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