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TEMPLATE: add a fallback for new outputdir parameter #3798

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TEMPLATE: add a fallback for new outputdir parameter #3798

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e31b463
add a fallback for new outputdir parameter
mashehu Oct 3, 2025
1e98e6a
[automated] Update CHANGELOG.md
nf-core-bot Oct 3, 2025
0697847
require modules for publish_dir_mode
mashehu Oct 3, 2025
f122695
Merge branch 'add-outputdir-fallback' of github.com:mashehu/tools int…
mashehu Oct 3, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
- Template: Update nextflow.config to use environment variable for `hook_url` ([#3756](https://github.com/nf-core/tools/pull/3756))
- Update nf-test to 0.9.3 ([#3781](https://github.com/nf-core/tools/pull/3781))
- update release checklist to battle test pipeline template more ([#3788](https://github.com/nf-core/tools/pull/3788))
- add a fallback for new outputdir parameter ([#3798](https://github.com/nf-core/tools/pull/3798))

### Linting

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6 changes: 6 additions & 0 deletions nf_core/pipeline-template/nextflow.config
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Expand Up @@ -72,6 +72,12 @@ params {
{%- endif %}
}

// Fallback for new output syntax
outputDir = params.outdir
{%- if modules %}
workflow.output.mode = params.publish_dir_mode
{%- endif %}

{% if modules -%}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
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