[EXAMPLE] hello-nextflow: new Nextflow syntax (full) #742

ewels · 2025-12-03T15:27:43Z

I didn't really mean to do this, I was just sort of curious and prodding around with @claude, then one thing led to another, and here we are.. 🤷🏻

This PR includes *all* upcoming syntax changes. Primarily:

Workflow inputs (params) - typed
Workflow outputs
Typed process inputs

It is meant as a demonstrator of what kind of changes will be needed for the training material - I'm not expecting that we merge as-is. It's possible that we can slice off some of this work and repackage in another PR to kickstart the update process.

@ewels

Mostly written by Claude, with some guiding and edits from @ewels. Solutions scripts tested, but material not read and checked in detail yet.

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github-actions · 2025-12-03T15:28:28Z

Nextflow linting complete!

❌ 4 files had 23 errors
✅ 152 files had no errors

^{💡 Tip: Click filename locations to go directly to that code.}

View all 23 issues

Type	Location	Message
Error	hello-nf-core/solutions/composable-hello/hello.nf:11:1	Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/composable-hello/modules/sayHello.nf'
Error	hello-nf-core/solutions/composable-hello/hello.nf:12:1	Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/composable-hello/modules/convertToUpper.nf'
Error	hello-nf-core/solutions/composable-hello/hello.nf:13:1	Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/composable-hello/modules/collectGreetings.nf'
Error	hello-nf-core/solutions/composable-hello/hello.nf:14:1	Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/composable-hello/modules/cowpy.nf'
Error	hello-nf-core/solutions/composable-hello/hello.nf:24:5	`sayHello` is not defined
Error	hello-nf-core/solutions/composable-hello/hello.nf:27:5	`convertToUpper` is not defined
Error	hello-nf-core/solutions/composable-hello/hello.nf:27:20	`sayHello` is not defined
Error	hello-nf-core/solutions/composable-hello/hello.nf:30:5	`collectGreetings` is not defined
Error	hello-nf-core/solutions/composable-hello/hello.nf:30:22	`convertToUpper` is not defined
Error	hello-nf-core/solutions/composable-hello/hello.nf:33:5	`cowpy` is not defined
Error	hello-nf-core/solutions/composable-hello/hello.nf:33:11	`collectGreetings` is not defined
Error	hello-nf-core/solutions/composable-hello/hello.nf:36:20	`cowpy` is not defined
Error	hello-nf-core/solutions/core-hello-part2/nextflow.config:154:17	Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/core-hello-part2/conf/test_full.config'
Error	side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:1:1	Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/validate_name.nf'
Error	side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:2:1	Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/say_hello.nf'
Error	side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:3:1	Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/timestamp_greeting.nf'
Error	side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:11:24	`VALIDATE_NAME` is not defined
Error	side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:12:24	`SAY_HELLO` is not defined
Error	side-quests/solutions/workflows_of_workflows/workflows/greeting.nf:13:26	`TIMESTAMP_GREETING` is not defined
Error	side-quests/solutions/workflows_of_workflows/workflows/transform.nf:1:1	Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/say_hello_upper.nf'
Error	side-quests/solutions/workflows_of_workflows/workflows/transform.nf:2:1	Invalid include source: '/home/runner/work/training/training/side-quests/solutions/workflows_of_workflows/modules/reverse_text.nf'
Error	side-quests/solutions/workflows_of_workflows/workflows/transform.nf:10:20	`SAY_HELLO_UPPER` is not defined
Error	side-quests/solutions/workflows_of_workflows/workflows/transform.nf:11:23	`REVERSE_TEXT` is not defined

vdauwera · 2025-12-03T15:46:04Z

docs/hello_nextflow/00_orientation.md

+Set the following environment variable before running any workflows:
+
+```bash
+export NXF_SYNTAX_PARSER=v2


Are we going to set this by default in the training environment? If so, can we make this a much shorter note to tell people running in their own environment to check requirements for local installation, and have the details live there? I really don't want to add a half page of warnings about previews and syntax requirements in a beginner training intro.

We can do, but that'll tell Nextflow to use the new syntax parser for all the training courses. Which we don't want yet, until they're all updated.

This is where timelines matter. This will become the default in 2026, so won't be needed from that point onwards. So if we're fast at updating all the courses, then yes - let's stick it into the dev environment. If not, then I think we need to tell people to do it themselves.

Probably the most user-friendly way to do this is to have an interactive script that runs on codespaces init that prompts the user to ask which course they're doing, then sets some env variables accordingly.

Or, *controvercy alert*, we split up the courses into separate repos and/or containers and have one per course.

Hahaha I hate both of those options. I don't want to have major differences in requirements for different courses except for specific super advanced topics, and they all have to work within a single environment.

So we just update syntax for everything in one go. It's the most sane option for end-users.

pditommaso

I do not think we should include preview features in the training material

vdauwera · 2025-12-03T16:33:36Z

I do not think we should include preview features in the training material

Completely agree. We've discussed this over slack and are making a plan to do the updates for released features now (use strict syntax across all courses) and another batch mid-year once the preview features are released.

ewels · 2025-12-03T16:39:43Z

I do not think we should include preview features in the training material

Yeah apologies - I opened the PR in tandem with an ongoing Slack thread so the context there was clear, but not when seeing the PR stand alone. I've updated the PR description and status to make this clear.

Not intending to merge this PR

pditommaso · 2025-12-03T16:44:35Z

Awesome, thanks 🙏

bentsherman · 2025-12-03T16:54:24Z

docs/hello_nextflow/01_hello_world.md


    output:
-        path 'output.txt'
+    file 'output.txt'


Minor point since typed processes shouldn't be used here until they are stable, but the "canonical" syntax here should use parentheses because it is just a function call returning a value, not a type qualifier like in the old process syntax

Worth updating the docs in that case?

I think the docs are pretty clear

Sorry, too many types!

bentsherman · 2025-12-03T16:56:06Z

hello-nextflow/hello-config.nf

+nextflow.preview.types = true
+


Not needed here. Did the language server add this? It should only add this flag if there were processes that were auto-converted

No this was me / claude being over-zealous in adding it. I didn't do any language server auto-correction here.

ewels · 2025-12-03T17:00:46Z

Ok I pulled out the parts of this PR that are for inputs + outputs + strict syntax and put them into a separate PR: #743

Can leave this one here for future reference if we want, or just close it out (can always refer to it in closed state).

vdauwera · 2025-12-03T17:12:51Z

Ok I pulled out the parts of this PR that are for inputs + outputs + strict syntax and put them into a separate PR: #743

Can leave this one here for future reference if we want, or just close it out (can always refer to it in closed state).

Let's close it out to avoid confusion

ewels added 4 commits December 3, 2025 14:44

Copy missing modules to solutions 5 + 6

abeeb55

Fix linting errors

2a2d6c4

Copy script to 6-hello-config so it's a complete example

f6c8ccb

Update hello-nextflow to use new language syntax features.

f4a66e4

Mostly written by Claude, with some guiding and edits from @ewels. Solutions scripts tested, but material not read and checked in detail yet.

vdauwera reviewed Dec 3, 2025

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pditommaso previously requested changes Dec 3, 2025

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ewels marked this pull request as draft December 3, 2025 16:36

ewels changed the title ~~hello-nextflow: new Nextflow syntax~~ [EXAMPLE] hello-nextflow: new Nextflow syntax (full) Dec 3, 2025

bentsherman reviewed Dec 3, 2025

View reviewed changes

ewels mentioned this pull request Dec 3, 2025

Hello nextflow: New workflow inputs + outputs + strict syntax #743

Open

ewels closed this Dec 3, 2025

ewels deleted the nextflow-hello-new-syntax branch December 3, 2025 17:35

		nextflow.preview.types = true

[EXAMPLE] hello-nextflow: new Nextflow syntax (full) #742

[EXAMPLE] hello-nextflow: new Nextflow syntax (full) #742

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