From 6bca1ef6ac4a2d3531f9bcd6855514e0d221454c Mon Sep 17 00:00:00 2001
From: Leila Mansouri <leilosky@hotmail.com>
Date: Wed, 22 Nov 2023 11:58:22 +0100
Subject: [PATCH] parametrised test data

---
 conf/tests/full/test_full.config            |  8 ++++----
 conf/tests/full/test_full_family.config     | 10 +++++-----
 conf/tests/full/test_full_multi_hpo.config  | 10 +++++-----
 conf/tests/full/test_full_single_vcf.config | 12 ++++++------
 4 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/conf/tests/full/test_full.config b/conf/tests/full/test_full.config
index ced51fd..d558386 100644
--- a/conf/tests/full/test_full.config
+++ b/conf/tests/full/test_full.config
@@ -1,9 +1,9 @@
 params {
     input           = "${params.reference_data_bucket}/pipelines/parabricks/germline/output/HG001-NA12878-pFDA_S1_L001_20k.vcf"
-    // input = 'https://lifebit-featured-datasets.s3-eu-west-1.amazonaws.com/pipelines/parabricks/germline/output/HG001-NA12878-pFDA_S1_L001_20k.vcf'
-    sample_name     = 'HG001_NA12878'
+    // input = "https://lifebit-featured-datasets.s3-eu-west-1.amazonaws.com/pipelines/parabricks/germline/output/HG001-NA12878-pFDA_S1_L001_20k.vcf"
+    sample_name     = "HG001_NA12878"
     hpo_terms_file  = "${params.reference_data_bucket}/pipelines/exomiser-nf/hpo_terms_file.txt"
-    prioritisers    = 'hiPhivePrioritiser'
-    exomiser_profile_files = 'full'
+    prioritisers    = "hiPhivePrioritiser"
+    exomiser_profile_files = "full"
     application_properties = "${params.reference_data_bucket}/pipelines/exomiser-nf/application.properties"
 }
diff --git a/conf/tests/full/test_full_family.config b/conf/tests/full/test_full_family.config
index 0944699..d1fca82 100644
--- a/conf/tests/full/test_full_family.config
+++ b/conf/tests/full/test_full_family.config
@@ -1,7 +1,7 @@
 params {
-    families_file     = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/fam_file.tsv'
-    prioritisers    = 'hiPhivePrioritiser'
-    exomiser_profile_files = 'full'
-    application_properties = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/application.properties'
-    auto_config_yml = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/auto_config.yml'
+    families_file     = "${params.reference_data_bucket}/pipelines/exomiser-nf/fam_file.tsv"
+    prioritisers    = "hiPhivePrioritiser"
+    exomiser_profile_files = "full"
+    application_properties = "${params.reference_data_bucket}/pipelines/exomiser-nf/application.properties"
+    auto_config_yml = "${params.reference_data_bucket}/pipelines/exomiser-nf/auto_config.yml"
 }
diff --git a/conf/tests/full/test_full_multi_hpo.config b/conf/tests/full/test_full_multi_hpo.config
index d57052b..97c4662 100644
--- a/conf/tests/full/test_full_multi_hpo.config
+++ b/conf/tests/full/test_full_multi_hpo.config
@@ -1,7 +1,7 @@
 params {
-    families_file     = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/fam_file_multi_hpo.tsv'
-    prioritisers    = 'hiPhivePrioritiser'
-    exomiser_profile_files = 'full'
-    application_properties = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/application.properties'
-    auto_config_yml = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/auto_config.yml'
+    families_file     = "${params.reference_data_bucket}/pipelines/exomiser-nf/fam_file_multi_hpo.tsv"
+    prioritisers    = "hiPhivePrioritiser"
+    exomiser_profile_files = "full"
+    application_properties = "${params.reference_data_bucket}/pipelines/exomiser-nf/application.properties"
+    auto_config_yml = "${params.reference_data_bucket}/pipelines/exomiser-nf/auto_config.yml"
 }
diff --git a/conf/tests/full/test_full_single_vcf.config b/conf/tests/full/test_full_single_vcf.config
index 050c6ad..946b9d7 100644
--- a/conf/tests/full/test_full_single_vcf.config
+++ b/conf/tests/full/test_full_single_vcf.config
@@ -1,8 +1,8 @@
 params {
-    families_file     = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/single_vcf.tsv'
-    hpo_terms_file  = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/hpo_terms_file.txt'
-    prioritisers    = 'hiPhivePrioritiser'
-    exomiser_profile_files = 'full'
-    application_properties = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/application.properties'
-    auto_config_yml = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/auto_config.yml'
+    families_file     = "${params.reference_data_bucket}/pipelines/exomiser-nf/single_vcf.tsv"
+    hpo_terms_file  = "${params.reference_data_bucket}/pipelines/exomiser-nf/hpo_terms_file.txt"
+    prioritisers    = "hiPhivePrioritiser"
+    exomiser_profile_files = "full"
+    application_properties = "${params.reference_data_bucket}/pipelines/exomiser-nf/application.properties"
+    auto_config_yml = "${params.reference_data_bucket}/pipelines/exomiser-nf/auto_config.yml"
 }