added testing profile for multi_hpo

lifebit-ai · Nov 2, 2023 · b266fee · b266fee
1 parent 5ef94b8
commit b266fee
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Showing 4 changed files with 9 additions and 2 deletions.
diff --git a/conf/family_test.config b/conf/family_test.config
@@ -1,6 +1,5 @@
 params {
     families_file     = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/fam_file.tsv'
-    hpo_terms_file  = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/hpo_terms_file.txt'
     prioritisers    = 'hiPhivePrioritiser'
     exomiser_data   = "s3://lifebit-featured-datasets/pipelines/exomiser-data-bundle"
     application_properties = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/application.properties'

diff --git a/conf/multi_hpo_test.config b/conf/multi_hpo_test.config
@@ -0,0 +1,7 @@
+params {
+    families_file     = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/fam_file_multi_hpo.tsv'
+    prioritisers    = 'hiPhivePrioritiser'
+    exomiser_data   = "s3://lifebit-featured-datasets/pipelines/exomiser-data-bundle"
+    application_properties = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/application.properties'
+    auto_config_yml = 's3://lifebit-featured-datasets/pipelines/exomiser-nf/auto_config.yml'
+}
diff --git a/nextflow.config b/nextflow.config
@@ -68,6 +68,7 @@ profiles {
    standard { includeConfig params.config }
    test_family { includeConfig 'conf/family_test.config' }
    test_single_vcf { includeConfig 'conf/single_vcf_test.config' }
+   test_multi_hpo { includeConfig 'conf/multi_hpo_test.config' }
    awsbatch { includeConfig 'conf/executors/awsbatch.config' }
    eu_west_1 { includeConfig 'conf/cloud-region/eu_west_1.config' }
    eu_west_2 { includeConfig 'conf/cloud-region/eu_west_2.config' }

diff --git a/testdata/fam_file_multi_hpo.tsv b/testdata/fam_file_multi_hpo.tsv
@@ -1,2 +1,2 @@
 run_id	proband_id	hpo	vcf_path	vcf_index_path	proband_sex	mother_id	father_id
-EX001	ERR3239334	HP:0001156; HP:0001363; HP:0011304  s3://lifebit-featured-datasets/pipelines/exomiser-nf/family_ERR3239334_ERR3989341_ERR3989342_small.vcf.gz	s3://lifebit-featured-datasets/pipelines/exomiser-nf/family_ERR3239334_ERR3989341_ERR3989342_small.vcf.gz.tbi	M	ERR3989342	ERR3989341
+EX001	ERR3239334	HP:0001156,HP:0001363,HP:0011304	s3://lifebit-featured-datasets/pipelines/exomiser-nf/family_ERR3239334_ERR3989341_ERR3989342_small.vcf.gz	s3://lifebit-featured-datasets/pipelines/exomiser-nf/family_ERR3239334_ERR3989341_ERR3989342_small.vcf.gz.tbi	M	ERR3989342	ERR3989341