Hello nextflow: New workflow inputs + outputs + strict syntax

[ewels]

Rehash of #742 but without the typed process inputs (which are still in beta).

Should be a more realistic start at updating the materials for the near future. We can approach typed processes + record types in 2026.

Also ran the auto-formatter on the files, which works now that strict syntax is enforced. I used the default settings - no Harshil alignment etc.

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[github-actions]

Nextflow linting complete!

❌ 4 files had 23 errors
✅ 151 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