fix tests

.github/workflows/ci.yml

@@ -51,7 +51,7 @@ jobs:
           echo ${{ steps.list.outputs.components }}
 
   test:
-    name: "Test | ${{ matrix.nf_test_files }} | ${{ matrix.NXF_VER }} | ${{ matrix.profile }}"
+    name: "${{ matrix.nf_test_files }} | ${{ matrix.NXF_VER }} | ${{ matrix.profile }}"
     if: needs.changes.outputs.nf_test_files != '[]'
     needs: [changes]
     runs-on: ubuntu-latest

nextflow.config

@@ -31,7 +31,8 @@ params {
     help_full                    = false
     show_hidden                  = false
     version                      = false
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
+    pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/'
 
     // Config options
     config_profile_name          = null

nf-test.config

@@ -5,9 +5,6 @@ config {
     // nf-test directory including temporary files for each test
     workDir ".nf-test"
 
-    // Location of an optional nextflow.config file specific for executing tests
-    configFile "conf/test.config"
-
     // Run all test with defined profile(s) from the main nextflow.config
     profile "test"
 

subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test

@@ -11,21 +11,19 @@ nextflow_workflow {
             workflow {
                 """
                 version             = false
-                help                = false
                 validate_params     = false
                 monochrome_logs     = false
                 nextflow_cli_args   = []
                 outdir              = 'results'
                 ena_metadata_fields = null
 
                 input[0] = version
-                input[1] = help
-                input[2] = validate_params
-                input[3] = monochrome_logs
-                input[4] = nextflow_cli_args
-                input[5] = outdir
-                input[6] = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
-                input[7] = ena_metadata_fields
+                input[1] = validate_params
+                input[2] = monochrome_logs
+                input[3] = nextflow_cli_args
+                input[4] = outdir
+                input[5] = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
+                input[6] = ena_metadata_fields
                 """
             }
         }