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f82da67
Update linting
LouisLeNezet Feb 9, 2026
bbab190
Update sites/docs/src/content/docs/guidelines/components/subworkflows.md
LouisLeNezet Feb 9, 2026
5b7a170
Update sites/docs/src/content/docs/guidelines/components/subworkflows.md
LouisLeNezet Feb 9, 2026
53c74cc
Update sites/docs/src/content/docs/guidelines/components/subworkflows.md
LouisLeNezet Feb 9, 2026
91dd664
Merge branch 'main' into nextflow_lint
LouisLeNezet Feb 9, 2026
78ed68e
Update sites/docs/src/content/docs/guidelines/components/modules.md
LouisLeNezet Feb 9, 2026
8107401
Update sites/docs/src/content/docs/guidelines/components/modules.md
LouisLeNezet Feb 9, 2026
cdafda2
Update sites/docs/src/content/docs/guidelines/components/subworkflows.md
LouisLeNezet Feb 9, 2026
80ccab2
Switch to table
LouisLeNezet Feb 9, 2026
e4dfa7f
Fix orthograph
LouisLeNezet Feb 9, 2026
a7b2689
Update sites/docs/src/content/docs/guidelines/components/modules.md
LouisLeNezet Feb 12, 2026
8a68201
Update sites/docs/src/content/docs/guidelines/components/modules.md
LouisLeNezet Feb 12, 2026
a5bc14a
Update syntax guidelines for Nextflow code
LouisLeNezet Feb 12, 2026
89950a5
Add Nextflow lint command to guidelines
LouisLeNezet Feb 12, 2026
ad9b918
Improve formatting of Nextflow linting instructions
LouisLeNezet Feb 12, 2026
116f757
Merge branch 'main' into nextflow_lint
LouisLeNezet Feb 12, 2026
2b7266f
Fix formatting of code quality command instruction
LouisLeNezet Feb 12, 2026
8723eab
Fix formatting of command usage in subworkflows.md
LouisLeNezet Feb 12, 2026
a852073
Remove whitespace
LouisLeNezet Feb 12, 2026
0712472
Merge branch 'main' into nextflow_lint
LouisLeNezet Feb 12, 2026
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18 changes: 18 additions & 0 deletions sites/docs/src/content/docs/guidelines/components/modules.md
Original file line number Diff line number Diff line change
Expand Up @@ -952,3 +952,21 @@ Please keep the file sorted alphabetically.
### General module code formatting

All code MUST be aligned to follow the '[Harshil Alignment™️](/docs/contributing/code_editors_and_styling/harshil_alignment)' format.

To maintain code quality and prevent issues, all code MUST be free of Nextflow warnings and errors.
Utilize the following command to check your code:

```bash
nextflow lint modules/nf-core/module_name
```

Common issues to avoid:

| Old syntax | Prefered syntax |
| -------------------------------------------------------- | --------------------------------------------------- |
| Unused `def args = task.ext.args ?: ''{:groovy}` in stub | delete it |
| undeclared variable `my_variable{:groovy}` | add `def my_variable{:groovy}` |
| `input.collect{ it[1].name }{:groovy}` | `input.collect{ meta, file -> file.name }{:groovy}` |
| `for{:groovy}` loop | `.each{}{:groovy}` operator |

By following these guidelines, you will ensure that your code is compliant with Nextflow standards.
17 changes: 17 additions & 0 deletions sites/docs/src/content/docs/guidelines/components/subworkflows.md
Original file line number Diff line number Diff line change
Expand Up @@ -273,3 +273,20 @@ Please keep the file sorted alphabetically.
### General module code formatting

All code MUST be aligned to follow the '[Harshil Alignment™️](/docs/contributing/code_editors_and_styling/harshil_alignment)' format.

To maintain code quality and prevent issues, all code MUST be free of Nextflow warnings and errors.
Utilize the following command to check your code:

```bash
nextflow lint subworkflows/nf-core/subworkflow_name
```

CCommon issues to avoid:

| Old syntax | Prefered syntax |
| ------------------------------------------ | --------------------------------------------------- |
| undeclared variable `my_variable{:groovy}` | add `def my_variable{:groovy}` |
| `input.collect{ it[1].name }{:groovy}` | `input.collect{ meta, file -> file.name }{:groovy}` |
| `for{:groovy}` loop | `.each{}{:groovy}` operator |

By following these guidelines, you will ensure that your code is compliant with Nextflow standards.
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