Merge pull request #2931 from jfy133/testdata-config-path

Adds test data base path to classic test configs for more easily switching between test data location
nf-core · May 7, 2024 · 1c2ce6c · 1c2ce6c
2 parents 73bba51 + d4c8f36
commit 1c2ce6c
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Showing 5 changed files with 21 additions and 12 deletions.
diff --git a/CHANGELOG.md b/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 `--pipelines_testdata_base_path` parameter to more easily switch locations of test data in test configs (#2931)[https://github.com/nf-core/tools/pull/2931]
 - Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention ([#2936](https://github.com/nf-core/tools/pull/2936))
 - Template config: `conda.channels`, not `channels` ([#2950](https://github.com/nf-core/tools/pull/2950))
 - Handles multiple DOIs + doi.org resolver from manifest.doi ([#2946](https://github.com/nf-core/tools/pull/2946))

diff --git a/nf_core/pipeline-template/conf/test.config b/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  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
     {% if igenomes -%}
     // Genome references

diff --git a/nf_core/pipeline-template/conf/test_full.config b/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 = params.pipelines_testdata_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 = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
     {%- endif %}
 }
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
@@ -28,15 +28,16 @@ params {
     multiqc_methods_description = null
 
     // Boilerplate options
-    outdir                     = null
-    publish_dir_mode           = 'copy'
-    email                      = null
-    email_on_fail              = null
-    plaintext_email            = false
-    monochrome_logs            = false
-    hook_url                   = null
-    help                       = false
-    version                    = false
+    outdir                       = null
+    publish_dir_mode             = 'copy'
+    email                        = null
+    email_on_fail                = null
+    plaintext_email              = false
+    monochrome_logs              = false
+    hook_url                     = null
+    help                         = false
+    version                      = false
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
     // Config options
     config_profile_name        = null

diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
@@ -267,6 +267,13 @@
                     "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)."
+                },
+                "pipelines_testdata_base_path": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Base URL or local path to location of pipeline test dataset files",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
+                    "hidden": true
                 }
             }
         }