Merge pull request #465 from Emiller88/test-data-config

Add test_data config magic
nf-core · Dec 8, 2021 · 84c6e1b · 84c6e1b
2 parents 39f0974 + bfb0b7a
commit 84c6e1b
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Showing 5 changed files with 14 additions and 17 deletions.
diff --git 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' {
         }
     }
 }
diff --git 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
@@ -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
@@ -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",
         [])
-}
+}
diff --git a/tests/subworkflows/nf-core/vep_annotate/main.nf b/tests/subworkflows/nf-core/vep_annotate/main.nf
@@ -14,12 +14,12 @@ 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,
         "WBcel235",
         "caenorhabditis_elegans",
         "104",
         [])
-}
+}