From f06790c3dec3eb4a8aea62b3290361ffae33375b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 10:45:36 +0200
Subject: [PATCH 1/6] add pipeline level tests

---
 conf/test.config       |  2 +-
 tests/main.nf.test     | 27 +++++++++++++++++++++++++++
 tests/sra_ids_test.csv |  7 +++++++
 3 files changed, 35 insertions(+), 1 deletion(-)
 create mode 100644 tests/main.nf.test
 create mode 100644 tests/sra_ids_test.csv

diff --git a/conf/test.config b/conf/test.config
index cb77f578..67291b47 100644
--- a/conf/test.config
+++ b/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  = 'tests/sra_ids_test.csv'
 
     validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
 }
diff --git a/tests/main.nf.test b/tests/main.nf.test
new file mode 100644
index 00000000..7bf19f34
--- /dev/null
+++ b/tests/main.nf.test
@@ -0,0 +1,27 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+
+    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 }
+            )
+        }
+    }
+
+}
diff --git a/tests/sra_ids_test.csv b/tests/sra_ids_test.csv
new file mode 100644
index 00000000..ec8b5cc9
--- /dev/null
+++ b/tests/sra_ids_test.csv
@@ -0,0 +1,7 @@
+SRR9984183
+SRR13191702
+ERR1160846
+SRR12848126
+SRR14593545
+SRR14709033
+GSE214215

From 6f94f654f3568a93a4dc319bb8e620cca1c50a9e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 11:07:14 +0200
Subject: [PATCH 2/6] add tags

---
 tests/tags.yml | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 tests/tags.yml

diff --git a/tests/tags.yml b/tests/tags.yml
new file mode 100644
index 00000000..3a1868da
--- /dev/null
+++ b/tests/tags.yml
@@ -0,0 +1,4 @@
+pipeline_fetchngs:
+  - **.nf
+  - **.config
+  - **.nf.test

From e9917d81b017d73d7c929ff6fcbadeff3aec018b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 11:17:19 +0200
Subject: [PATCH 3/6] update tags

---
 tests/tags.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/tags.yml b/tests/tags.yml
index 3a1868da..5b091f8e 100644
--- a/tests/tags.yml
+++ b/tests/tags.yml
@@ -1,4 +1,4 @@
 pipeline_fetchngs:
-  - **.nf
-  - **.config
-  - **.nf.test
+  - "**.nf"
+  - "**.config"
+  - "**.nf.test"

From 91d59aa6251cb68a695d48901ee5e6fb4e72acad Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 11:37:48 +0200
Subject: [PATCH 4/6] use proper tag

---
 tests/main.nf.test | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 7bf19f34..ac05aea9 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test pipeline"
     script "../main.nf"
     tag "pipeline"
+    tag "pipeline_fetchngs"
 
     test("Run with profile test") {
 

From 796728a52184426ba3c8a5761d16a8b7b321b5ae Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Oct 2023 11:38:44 +0200
Subject: [PATCH 5/6] extends files to trigger test

---
 tests/tags.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/tags.yml b/tests/tags.yml
index 5b091f8e..80e5fd75 100644
--- a/tests/tags.yml
+++ b/tests/tags.yml
@@ -2,3 +2,4 @@ pipeline_fetchngs:
   - "**.nf"
   - "**.config"
   - "**.nf.test"
+  - "**.json"

From 8b6570b3a1cf7575721f51dead316b591c66d7e5 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Fri, 13 Oct 2023 12:23:23 +0200
Subject: [PATCH 6/6] Update conf/test.config

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 conf/test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test.config b/conf/test.config
index 67291b47..c09a571c 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input  = 'tests/sra_ids_test.csv'
+    input  = '${projectDir}/tests/sra_ids_test.csv'
 
     validationSchemaIgnoreParams = 'test_data_base,merge_samplesheet_ids,fastq_ftp_ids,test_data'
 }