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Use variable for includeConfig to avoid ternary expression #3343

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Use variable for includeConfig to avoid ternary expression #3343

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9 changes: 6 additions & 3 deletions nf_core/pipeline-template/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -210,11 +210,13 @@ profiles {

{% if nf_core_configs -%}
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
custom_config_url = !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
includeConfig custom_config_url

// Load {{ name }} custom profiles from different institutions.
// 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 ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
// custom_pipeline_config_url = !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null"
// includeConfig custom_pipeline_config_url
{%- endif %}

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
Expand All @@ -228,7 +230,8 @@ charliecloud.registry = 'quay.io'

{% if igenomes -%}
// Load igenomes.config if required
includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
igenomes_config_path = !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
includeConfig igenomes_config_path
{%- endif %}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
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