add pipeline level tests

conf/test.config

@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
+    input  = '${projectDir}/tests/sra_ids_test.csv'
 
     validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
 }

tests/main.nf.test

@@ -0,0 +1,28 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_fetchngs"
+
+    test("Run with profile test") {
+
+        when {
+            params {
+                outdir     = "results"
+                max_cpus   = 2
+                max_memory = '6.GB'
+                max_time   = '6.h'
+                input      = "$projectDir/tests/sra_ids_test.csv"
+                validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+}

tests/sra_ids_test.csv

@@ -0,0 +1,7 @@
+SRR9984183
+SRR13191702
+ERR1160846
+SRR12848126
+SRR14593545
+SRR14709033
+GSE214215

tests/tags.yml

@@ -0,0 +1,5 @@
+pipeline_fetchngs:
+  - "**.nf"
+  - "**.config"
+  - "**.nf.test"
+  - "**.json"