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remove try-catch blocks from nextflow.config
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mirpedrol committed Sep 13, 2024
1 parent 8e47a33 commit 733e9b3
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Showing 2 changed files with 4 additions and 10 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -38,6 +38,7 @@
- add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
- run nf-core lint `--release` on PRs to master ([#3148](https://github.com/nf-core/tools/pull/3148))
- Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
- Remove try/catch blocks from `nextflow.config` ([#3167](https://github.com/nf-core/tools/pull/3167))

### Linting

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13 changes: 3 additions & 10 deletions nf_core/pipeline-template/nextflow.config
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Expand Up @@ -84,18 +84,11 @@ process {
{% endif %}
{% if nf_core_configs -%}
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

// Load {{ name }} custom profiles from different institutions.
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: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
}
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
{% endif -%}

profiles {
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