update all test config input paths

nf-core · May 15, 2024 · 673a805 · 673a805
1 parent e2cf136
commit 673a805
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Showing 10 changed files with 10 additions and 10 deletions.
diff --git a/conf/test_grch38.config b/conf/test_grch38.config
@@ -13,6 +13,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
     genome_reference = 'grch38'
 }
diff --git a/conf/test_mhcflurry.config b/conf/test_mhcflurry.config
@@ -16,6 +16,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
     tools = 'mhcflurry'
 }
diff --git a/conf/test_mhcnuggets.config b/conf/test_mhcnuggets.config
@@ -16,6 +16,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants_class1_and_2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants_class1_and_2.csv'
     tools = 'mhcnuggets-class-1,mhcnuggets-class-2'
 }
diff --git a/conf/test_netmhc.config b/conf/test_netmhc.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 
     tools = 'netmhc-4.0'
     netmhc_path = './non-free/netmhc.tar.gz'

diff --git a/conf/test_netmhcii.config b/conf/test_netmhcii.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
 
     tools = 'netmhcii-2.2'
     netmhcii_path = './non-free/netmhcii.tar.Z'

diff --git a/conf/test_netmhciipan.config b/conf/test_netmhciipan.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
 
     tools = 'netmhciipan-4.1'
     netmhciipan_path = './non-free/netmhciipan.tar.gz'

diff --git a/conf/test_netmhcpan.config b/conf/test_netmhcpan.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 
     tools = 'netmhcpan-4.0'
     netmhcpan_path = './non-free/netmhcpan.tar.gz'

diff --git a/conf/test_peptides.config b/conf/test_peptides.config
@@ -13,5 +13,5 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 }
diff --git a/conf/test_peptides_h2.config b/conf/test_peptides_h2.config
@@ -13,6 +13,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_mouse.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_mouse.csv'
     tools = 'mhcnuggets-class-1'
 }
diff --git a/conf/test_proteins.config b/conf/test_proteins.config
@@ -13,5 +13,5 @@ params {
     max_time = 4.h
 
     // Input data
-    input = 'https://github.com/nf-core/test-datasets/raw/epitopeprediction/testdata/sample_sheets/sample_sheet_proteins.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_proteins.csv'
 }