Adds test data base path to classic test configs for more easily switching between test data location

CHANGELOG.md

@@ -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))
+- Add a new hidden `--test_data_base_path` parameter to more easily switch locations of test data in test configs (#2900)[]
 
 ### Linting
 

nf_core/pipeline-template/conf/test.config

@@ -22,7 +22,7 @@ params {
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input  = test_data_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
     {% if igenomes -%}
     // Genome references

nf_core/pipeline-template/conf/test_full.config

@@ -17,13 +17,13 @@ params {
     // Input data for full size test
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    input = test_data_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
 
     {% if igenomes -%}
     // Genome references
     genome = 'R64-1-1'
     {%- else -%}
     // Fasta references
-    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
+    fasta = test_data_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
     {%- endif %}
 }

nf_core/pipeline-template/nextflow.config

@@ -37,6 +37,7 @@ params {
     hook_url                   = null
     help                       = false
     version                    = false
+    test_data_base_path        = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
     // Config options
     config_profile_name        = null

nf_core/pipeline-template/nextflow_schema.json

@@ -267,6 +267,12 @@
                     "description": "Validation of parameters in lenient more.",
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
+                },
+                "test_data_base_path": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Base URL or local path to location of pipeline test dataset files",
+                    "hidden": true,
                 }
             }
         }