Merge pull request #601 from asp8200/update_sentieon_dnascope_model

Updating Sentieon DNAscope ml-model
nf-core · Aug 21, 2024 · d635171 · d635171
2 parents 243c4b1 + fbf2d4f
commit d635171
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Showing 4 changed files with 4 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Updated the model for Sentieon DNAScope to v1.1 [#601](https://github.com/nf-core/raredisease/pull/601)
 - bwameme can no longer be used to align mitochondrial reads [#600](https://github.com/nf-core/raredisease/pull/600)
 - Males' X and Y chromosomes will be treated as haploids during variant calling by deepvariant [#598](https://github.com/nf-core/raredisease/pull/598)
 - Acceptable type for lane field in the samplesheet from number to string [#597](https://github.com/nf-core/raredisease/pull/597)

diff --git a/conf/test.config b/conf/test.config
@@ -40,7 +40,7 @@ params {
     intervals_wgs        = params.pipelines_testdata_base_path + 'raredisease/reference/target_wgs.interval_list'
     intervals_y          = params.pipelines_testdata_base_path + 'raredisease/reference/targetY.interval_list'
     known_dbsnp          = params.pipelines_testdata_base_path + 'raredisease/reference/dbsnp_-138-.vcf.gz'
-    ml_model             = 'https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model'
+    ml_model             = 'https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model'
     mobile_element_references       = params.pipelines_testdata_base_path + 'raredisease/reference/mobile_element_references.tsv'
     mobile_element_svdb_annotations = params.pipelines_testdata_base_path + 'raredisease/reference/svdb_querydb_files.csv'
     reduced_penetrance   = params.pipelines_testdata_base_path + 'raredisease/reference/reduced_penetrance.tsv'

diff --git a/conf/test_one_sample.config b/conf/test_one_sample.config
@@ -40,7 +40,7 @@ params {
     intervals_wgs        = params.pipelines_testdata_base_path + 'raredisease/reference/target_wgs.interval_list'
     intervals_y          = params.pipelines_testdata_base_path + 'raredisease/reference/targetY.interval_list'
     known_dbsnp          = params.pipelines_testdata_base_path + 'raredisease/reference/dbsnp_-138-.vcf.gz'
-    ml_model             = 'https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model'
+    ml_model             = 'https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model'
     mobile_element_references       = params.pipelines_testdata_base_path + 'raredisease/reference/mobile_element_references.tsv'
     mobile_element_svdb_annotations = params.pipelines_testdata_base_path + 'raredisease/reference/svdb_querydb_files.csv'
     reduced_penetrance   = params.pipelines_testdata_base_path + 'raredisease/reference/reduced_penetrance.tsv'

diff --git a/conf/test_sentieon.config b/conf/test_sentieon.config
@@ -38,7 +38,7 @@ params {
     intervals_wgs        = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list"
     intervals_y          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list"
     known_dbsnp          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
-    ml_model             = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
+    ml_model             = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model"
     mobile_element_references = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv"
     mobile_element_svdb_annotations = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv"
     reduced_penetrance   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"