From 78ab498a32666b069ea940d57e461969c16f9fd6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Oct 2023 11:50:17 +0200
Subject: [PATCH 1/3] Add .gitignore to files_unchanged

---
 .nf-core.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index ee325600a3..36189e1fcb 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -5,6 +5,7 @@ lint:
     - .github/workflows/awsfulltest.yml
     - conf/modules.config
   files_unchanged:
+    - .gitignore
     - assets/nf-core-sarek_logo_light.png
     - docs/images/nf-core-sarek_logo_dark.png
     - docs/images/nf-core-sarek_logo_light.png

From d9b2293d616cbe47b184177d86e65f2aed77b5b6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Oct 2023 16:37:01 +0200
Subject: [PATCH 2/3] Minor fixes for nf-test

---
 CHANGELOG.md       |  1 +
 tests/main.nf.test | 13 +++++++------
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 56f7f6249c..7b8c7f3b33 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module
 - [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline
 - [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev
+- [###]() - Add nf-test for whole pipeline.
 
 ### Changed
 
diff --git a/tests/main.nf.test b/tests/main.nf.test
index 1b4e18a2e0..ad9209ab88 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -9,12 +9,13 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir     = "results"
-                max_cpus   = 2
-                max_memory = '6.GB'
-                max_time   = '6.h'
-                input      = "$projectDir/tests/csv/3.0/fastq_pair.csv"
-                validationSchemaIgnoreParams = 'test_data_base,test_data'
+                outdir                       = "results"
+                max_cpus                     = 2
+                max_memory                   = '6.GB'
+                max_time                     = '6.h'
+                input                        = "$projectDir/tests/csv/3.0/fastq_pair.csv"
+                validationSchemaIgnoreParams = 'test_data_base,test_data,genomes'
+                use_gatk_spark               = false
             }
         }
 

From 67901679aeebba7cb1e89ccae639182c7dd89a53 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Tue, 17 Oct 2023 17:48:29 +0200
Subject: [PATCH 3/3] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7b8c7f3b33..c00837cf16 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1113](https://github.com/nf-core/sarek/pull/1113) - Adding CNVkit genemetrics module
 - [#1193](https://github.com/nf-core/sarek/pull/1193) - Adding support for Sentieon's DnaScope for germline variant-calling including joint-germline
 - [#1271](https://github.com/nf-core/sarek/pull/1271) - Back to dev
-- [###]() - Add nf-test for whole pipeline.
+- [#1290](https://github.com/nf-core/sarek/pull/1290) - Add nf-test for whole pipeline.
 
 ### Changed