From 673a805f3a70593c8c9ca16cc7d173625ce7dc68 Mon Sep 17 00:00:00 2001 From: Christopher Mohr Date: Wed, 15 May 2024 07:05:42 +0000 Subject: [PATCH] update all test config input paths --- conf/test_grch38.config | 2 +- conf/test_mhcflurry.config | 2 +- conf/test_mhcnuggets.config | 2 +- conf/test_netmhc.config | 2 +- conf/test_netmhcii.config | 2 +- conf/test_netmhciipan.config | 2 +- conf/test_netmhcpan.config | 2 +- conf/test_peptides.config | 2 +- conf/test_peptides_h2.config | 2 +- conf/test_proteins.config | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/conf/test_grch38.config b/conf/test_grch38.config index 0c2bbd0..4740d3c 100644 --- 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 index 7558693..3cab934 100644 --- 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 index 90774b5..bd51993 100644 --- 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 index 1ad878a..56cf70f 100644 --- 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 index 2cc2804..1b58fb1 100644 --- 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 index 07b2781..30e3a7d 100644 --- 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 index 2e9fb4f..b1bc950 100644 --- 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 index 74c98f3..499b31d 100644 --- 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 index 26a4e00..21582dd 100644 --- 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 index 7515999..084c75b 100644 --- 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' }