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mashehu merged 2 commits into from
Apr 15, 2026
Merged

Update example links in main.nf comments #4188

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Update example links in main.nf comments
mashehu Apr 15, 2026
dbe8232
[automated] Update CHANGELOG.md
nf-core-bot Apr 15, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -54,6 +54,7 @@
- Remove deprecated cli commands and --migrate-pytest flag with all obsoleted code. ([4167](https://github.com/nf-core/tools/pull/4167))
- Remove `--migrate-pytest` functionality and deprecated pipeline commands ([#4167](https://github.com/nf-core/tools/pull/4167))
- Add more ruff rules (B, PTH) ([#4034](https://github.com/nf-core/tools/pull/4034))
- Update example links in main.nf comments ([#4188](https://github.com/nf-core/tools/pull/4188))

### Linting

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4 changes: 2 additions & 2 deletions nf_core/module-template/main.nf
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Expand Up @@ -126,8 +126,8 @@ process {{ component_name_underscore|upper }} {
{% if not_empty_template -%}
// TODO nf-core: A stub section should mimic the execution of the original module as best as possible
// Have a look at the following examples:
// Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
// Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
// Simple example: https://github.com/nf-core/modules/blob/624977dfaf562211e68a8a868ca80acc8461f1ac/modules/nf-core/cutadapt/main.nf#L34-L46
// Complex example: https://github.com/nf-core/modules/blob/88d43dad73a675e66bff49ebb57fe657a5909018/modules/nf-core/bedtools/split/main.nf#L32-L43
// TODO nf-core: If the module doesn't use arguments ($args), you SHOULD remove:
// - The definition of args `def args = task.ext.args ?: ''` above.
// - The use of the variable in the script `echo $args ` below.
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