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Activate pipeline institutional configs in template #2936

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merged 4 commits into from
May 2, 2024
Merged

Activate pipeline institutional configs in template #2936

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aaabf5f
Update nextflow.config
jfy133 Apr 26, 2024
f1ce816
Update CHANGELOG.md
jfy133 Apr 26, 2024
c83cdfa
Apply suggestions from code review
jfy133 Apr 26, 2024
91d264b
[automated] Fix code linting
nf-core-bot Apr 26, 2024
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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 @@ -13,6 +13,7 @@
- Update python to 3.12 ([#2805](https://github.com/nf-core/tools/pull/2805))
- Remove `pyproject.toml` from template root
- Shorten lines in pipeline template ([#2908](https://github.com/nf-core/tools/pull/2908))
- Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention ([#2936](https://github.com/nf-core/tools/pull/2936))

### Linting

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11 changes: 5 additions & 6 deletions nf_core/pipeline-template/nextflow.config
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Expand Up @@ -76,12 +76,11 @@ try {
}

// Load {{ name }} custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
// }
try {
includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
}
{% endif -%}

profiles {
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