From a225aeba7826ba6c9742d3beb88283091a457cbc Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Tue, 7 Dec 2021 13:00:52 -0600
Subject: [PATCH 1/2] test: Pull in test_data config

---
 tests/config/test_data.config | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 9395e7626c..665947a594 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -1,18 +1,15 @@
 def test_data_dir = "${launchDir}/tests/data/"
 def nf_core_modules_data = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/"
 
+try {
+    includeConfig "https://raw.githubusercontent.com/nf-core/modules/master/tests/config/test_data.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/modules test data config")
+}
+
 params {
     test_data {
-        'nf-core' {
-            'bed' {
-                test_bed               = "${nf_core_modules_data}/genomics/sarscov2/genome/bed/test.bed"
-                test2_bed              = "${nf_core_modules_data}/genomics/sarscov2/genome/bed/test2.bed"
-            }
-            genome_fasta               = "${nf_core_modules_data}/genomics/sarscov2/genome/genome.fasta"
-            genome_sizes               = "${nf_core_modules_data}/genomics/sarscov2/genome/genome.sizes"
-            test_paired_end_sorted_bai = "${nf_core_modules_data}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai"
-            test_paired_end_sorted_bam = "${nf_core_modules_data}/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam"
-            test_vcf                   = "${nf_core_modules_data}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
+        'external' {
         }
     }
 }

From bfb0b7a588c08e6eadf249ea977ac5d907fd3ae6 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Tue, 7 Dec 2021 13:11:28 -0600
Subject: [PATCH 2/2] test: Update test_data calls

---
 tests/subworkflows/local/annotate/main.nf          | 2 +-
 tests/subworkflows/nf-core/markduplicates/main.nf  | 4 ++--
 tests/subworkflows/nf-core/snpeff_annotate/main.nf | 4 ++--
 tests/subworkflows/nf-core/vep_annotate/main.nf    | 4 ++--
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/subworkflows/local/annotate/main.nf b/tests/subworkflows/local/annotate/main.nf
index d959ef3470..a1138bd994 100644
--- a/tests/subworkflows/local/annotate/main.nf
+++ b/tests/subworkflows/local/annotate/main.nf
@@ -19,7 +19,7 @@ include { ANNOTATE } from '../../../../subworkflows/local/annotate' addParams(
 
 workflow test_annotate {
     input = [[id: 'test'],
-            [file(params.test_data['nf-core']['test_vcf'], checkIfExists: true)]]
+             [file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)]]
 
     ANNOTATE(
         input,
diff --git a/tests/subworkflows/nf-core/markduplicates/main.nf b/tests/subworkflows/nf-core/markduplicates/main.nf
index feb130c696..2e61829e0a 100644
--- a/tests/subworkflows/nf-core/markduplicates/main.nf
+++ b/tests/subworkflows/nf-core/markduplicates/main.nf
@@ -12,8 +12,8 @@ include { MARKDUPLICATES } from '../../../../subworkflows/nf-core/markduplicates
 
 workflow test_markduplicates {
     input = [[id: 'test'],
-            [file(params.test_data['nf-core']['test_paired_end_sorted_bam'], checkIfExists: true)],
-            [file(params.test_data['nf-core']['test_paired_end_sorted_bai'], checkIfExists: true)]]
+             [file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
+             [file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]]
 
     MARKDUPLICATES ( input, false, true )
 }
diff --git a/tests/subworkflows/nf-core/snpeff_annotate/main.nf b/tests/subworkflows/nf-core/snpeff_annotate/main.nf
index 5de360f0ee..56af76c5e6 100644
--- a/tests/subworkflows/nf-core/snpeff_annotate/main.nf
+++ b/tests/subworkflows/nf-core/snpeff_annotate/main.nf
@@ -14,10 +14,10 @@ include { SNPEFF_ANNOTATE } from '../../../../subworkflows/nf-core/snpeff_annota
 
 workflow test_snpeff_annotate {
     input = [[id: 'test'],
-            [file(params.test_data['nf-core']['test_vcf'], checkIfExists: true)]]
+            [file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)]]
 
     SNPEFF_ANNOTATE (
         input,
         "WBcel235.99",
         [])
-}
\ No newline at end of file
+}
diff --git a/tests/subworkflows/nf-core/vep_annotate/main.nf b/tests/subworkflows/nf-core/vep_annotate/main.nf
index 152bd23d76..268180ef3c 100644
--- a/tests/subworkflows/nf-core/vep_annotate/main.nf
+++ b/tests/subworkflows/nf-core/vep_annotate/main.nf
@@ -14,7 +14,7 @@ include { VEP_ANNOTATE } from '../../../../subworkflows/nf-core/vep_annotate' ad
 
 workflow test_vep_annotate {
     input = [[id: 'test'],
-            [file(params.test_data['nf-core']['test_vcf'], checkIfExists: true)]]
+            [file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)]]
 
     VEP_ANNOTATE (
         input,
@@ -22,4 +22,4 @@ workflow test_vep_annotate {
         "caenorhabditis_elegans",
         "104",
         [])
-}
\ No newline at end of file
+}