add ci profile to prevent server raise inside action

Author: BioWilko

.github/workflows/ci-tests.yml

@@ -2,7 +2,7 @@ name: CI Tests
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
 
 concurrency:
@@ -16,7 +16,7 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-      
+
       - name: Start Kraken Server
         run: |
           docker run -d --name kraken-server --network host \
@@ -38,7 +38,7 @@ jobs:
           sudo mv nf-test /usr/local/bin/
 
       - name: Run Tests
-        run: nf-test test --ci --profile docker,local --tag ci
+        run: nf-test test --ci --profile docker,local,ci --tag ci
 
       - name: upload logs
         if: always()
@@ -48,4 +48,4 @@ jobs:
           include-hidden-files: true
           path: ./.nf-test/*
           retention-days: 1
-          if-no-files-found: ignore
+          if-no-files-found: ignore

nextflow.config

@@ -127,6 +127,9 @@ profiles {
     local {
         includeConfig 'conf/local.config'
     }
+    ci {
+        raise_server = false
+    }
 }
 
 

tests/e2e/main.nf.test

@@ -11,7 +11,6 @@ nextflow_pipeline {
             params {
                 fastq = "${projectDir}/tests/test-data/barcode01/barcode01.fq.gz"
                 outdir = "$outputDir/single_long_read"
-                raise_server = false
                 kraken_database = [
                     "default": [
                         "name": "testdb-kraken2",