Merge pull request #24 from uclahs-cds/nwiltsie-verification-tests

Downgrade score, add proper verification tests
uclahs-cds · Sep 5, 2024 · f6f9a91 · f6f9a91
2 parents e547985 + 16dc70f
commit f6f9a91
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Showing 36 changed files with 430 additions and 96 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,8 +17,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Add reverse liftover (GRCh38 -> GRCh37) for SNV branch
 - Add reverse liftover (GRCh38 -> GRCh37) for SV branch
 - Add optional `target_threshold` and `target_specificity` parameters
+- Add NFTest cases for all variant callers and directions
 
 ### Changed
 
 - Sort VCF after liftover in SV branch
 - Hide parametric complexity behind simpler user inputs
+- Downgrade to score version 1.16
diff --git a/config/default.config b/config/default.config
@@ -17,7 +17,7 @@ params {
     docker_container_registry = "ghcr.io/uclahs-cds"
 
     // Docker images
-    bcftools_version   = '1.20_score-1.20-20240505'
+    bcftools_version   = '1.20_score-1.16-20221221'
     bedtools_version   = '2.31.0'
     gatk_version       = '4.4.0.0'
     pipeval_version    = '5.0.0-rc.3'

diff --git a/module/predict_stability.nf b/module/predict_stability.nf
@@ -43,13 +43,14 @@ process run_apply_stability_annotations {
     publishDir path: "${params.output_dir_base}/output",
         pattern: "{stability,filtered}.vcf.gz{,.tbi}",
         mode: "copy",
-        saveAs: { "${sample_id}-${it}" }
+        saveAs: { "${sample_id}-${variant_caller}-${it}" }
 
     input:
     tuple val(sample_id),
         path(annotated_vcf, stageAs: 'inputs/*'),
         path(stability_tsv, stageAs: 'inputs/*'),
         path(stability_tsv_tbi, stageAs: 'inputs/*')
+    val(variant_caller)
 
     output:
     tuple val(sample_id),
@@ -120,7 +121,8 @@ workflow workflow_predict_stability {
             compress_and_index_HTSlib.out.compressed_tsv_with_index,
             failOnDuplicate: true,
             failOnMismatch: true
-        )
+        ),
+        variant_caller
     )
 
     emit:

diff --git a/nftest.yml b/nftest.yml
@@ -3,26 +3,173 @@ global:
   temp_dir: test/work
   remove_temp: true
   clean_logs: true
-  nf_config: test/common.config
+  nf_config: nextflow.config
 
 cases:
-  - name: SNV
+  - name: HaplotypeCaller-37
     nf_script: ./main.nf
-    nf_config: test/snv.config
-    params_file: test/snv.yaml
+    nf_config: test/HaplotypeCaller-37.config
+    params_file: test/yamls/HaplotypeCaller-37.yaml
     skip: false
     verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_gSNP_HaplotypeCaller_StableLift-GRCh38.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-HaplotypeCaller-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_gSNP_HaplotypeCaller_StableLift-GRCh38_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-HaplotypeCaller-filtered.vcf.gz'
 
-  - name: SNV-backward
+  - name: Delly2-37
     nf_script: ./main.nf
-    nf_config: test/backward.config
-    params_file: test/snv-backward.yaml
+    nf_config: test/Delly2-37.config
+    params_file: test/yamls/Delly2-37.yaml
     skip: false
     verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_gSV_Delly2_StableLift-GRCh38.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-Delly2-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_gSV_Delly2_StableLift-GRCh38_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-Delly2-filtered.vcf.gz'
 
-  - name: SV
+  - name: Muse2-37
     nf_script: ./main.nf
-    nf_config: test/sv.config
-    params_file: test/sv.yaml
+    nf_config: test/Muse2-37.config
+    params_file: test/yamls/Muse2-37.yaml
     skip: false
     verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_sSNV_Muse2_StableLift-GRCh38.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-Muse2-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_sSNV_Muse2_StableLift-GRCh38_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-Muse2-filtered.vcf.gz'
+
+  - name: Mutect2-37
+    nf_script: ./main.nf
+    nf_config: test/Mutect2-37.config
+    params_file: test/yamls/Mutect2-37.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_sSNV_Mutect2_StableLift-GRCh38.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-Mutect2-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_sSNV_Mutect2_StableLift-GRCh38_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-Mutect2-filtered.vcf.gz'
+
+  - name: SomaticSniper-37
+    nf_script: ./main.nf
+    nf_config: test/SomaticSniper-37.config
+    params_file: test/yamls/SomaticSniper-37.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_sSNV_SomaticSniper_StableLift-GRCh38.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-SomaticSniper-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_sSNV_SomaticSniper_StableLift-GRCh38_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-SomaticSniper-filtered.vcf.gz'
+
+  - name: Strelka2-37
+    nf_script: ./main.nf
+    nf_config: test/Strelka2-37.config
+    params_file: test/yamls/Strelka2-37.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_sSNV_Strelka2_StableLift-GRCh38.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-Strelka2-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh37-to-GRCh38/TCGA-SARC_10TN-WGS_GRCh37_sSNV_Strelka2_StableLift-GRCh38_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh37/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh37-Strelka2-filtered.vcf.gz'
+
+  - name: HaplotypeCaller-38
+    nf_script: ./main.nf
+    nf_config: test/HaplotypeCaller-38.config
+    params_file: test/yamls/HaplotypeCaller-38.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_gSNP_HaplotypeCaller_StableLift-GRCh37.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-HaplotypeCaller-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_gSNP_HaplotypeCaller_StableLift-GRCh37_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-HaplotypeCaller-filtered.vcf.gz'
+
+  - name: Delly2-38
+    nf_script: ./main.nf
+    nf_config: test/Delly2-38.config
+    params_file: test/yamls/Delly2-38.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_gSV_Delly2_StableLift-GRCh37.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-Delly2-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_gSV_Delly2_StableLift-GRCh37_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-Delly2-filtered.vcf.gz'
+
+  - name: Muse2-38
+    nf_script: ./main.nf
+    nf_config: test/Muse2-38.config
+    params_file: test/yamls/Muse2-38.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_sSNV_Muse2_StableLift-GRCh37.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-Muse2-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_sSNV_Muse2_StableLift-GRCh37_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-Muse2-filtered.vcf.gz'
+
+  - name: Mutect2-38
+    nf_script: ./main.nf
+    nf_config: test/Mutect2-38.config
+    params_file: test/yamls/Mutect2-38.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_sSNV_Mutect2_StableLift-GRCh37.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-Mutect2-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_sSNV_Mutect2_StableLift-GRCh37_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-Mutect2-filtered.vcf.gz'
+
+  - name: SomaticSniper-38
+    nf_script: ./main.nf
+    nf_config: test/SomaticSniper-38.config
+    params_file: test/yamls/SomaticSniper-38.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_sSNV_SomaticSniper_StableLift-GRCh37.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-SomaticSniper-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_sSNV_SomaticSniper_StableLift-GRCh37_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-SomaticSniper-filtered.vcf.gz'
+
+  - name: Strelka2-38
+    nf_script: ./main.nf
+    nf_config: test/Strelka2-38.config
+    params_file: test/yamls/Strelka2-38.yaml
+    skip: false
+    verbose: true
+    asserts:
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_sSNV_Strelka2_StableLift-GRCh37.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-Strelka2-stability.vcf.gz'
+      - script: test/compare-VCFs.sh
+        expect: /hot/project/method/AlgorithmEvaluation/BNCH-000142-GRCh37v38/test/output/TCGA-SARC_10TN-WGS_GRCh38-to-GRCh37/TCGA-SARC_10TN-WGS_GRCh38_sSNV_Strelka2_StableLift-GRCh37_filtered.vcf.gz
+        actual: 'pipeline-StableLift-*/TCGA-SARC_10TN-WGS_GRCh38/StableLift-*/output/TCGA-SARC_10TN-WGS_GRCh38-Strelka2-filtered.vcf.gz'
diff --git a/test/Delly2-37.config b/test/Delly2-37.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "Delly2"
+    liftover_direction = "GRCh37ToGRCh38"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/Delly2-38.config b/test/Delly2-38.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "Delly2"
+    liftover_direction = "GRCh38ToGRCh37"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/HaplotypeCaller-37.config b/test/HaplotypeCaller-37.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "HaplotypeCaller"
+    liftover_direction = "GRCh37ToGRCh38"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/HaplotypeCaller-38.config b/test/HaplotypeCaller-38.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "HaplotypeCaller"
+    liftover_direction = "GRCh38ToGRCh37"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/Muse2-37.config b/test/Muse2-37.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "Muse2"
+    liftover_direction = "GRCh37ToGRCh38"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/Muse2-38.config b/test/Muse2-38.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "Muse2"
+    liftover_direction = "GRCh38ToGRCh37"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/Mutect2-37.config b/test/Mutect2-37.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "Mutect2"
+    liftover_direction = "GRCh37ToGRCh38"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/Mutect2-38.config b/test/Mutect2-38.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "Mutect2"
+    liftover_direction = "GRCh38ToGRCh37"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/SomaticSniper-37.config b/test/SomaticSniper-37.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "SomaticSniper"
+    liftover_direction = "GRCh37ToGRCh38"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/SomaticSniper-38.config b/test/SomaticSniper-38.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "SomaticSniper"
+    liftover_direction = "GRCh38ToGRCh37"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/Strelka2-37.config b/test/Strelka2-37.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "Strelka2"
+    liftover_direction = "GRCh37ToGRCh38"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()
diff --git a/test/Strelka2-38.config b/test/Strelka2-38.config
@@ -0,0 +1,13 @@
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/config/methods.config"
+includeConfig "${projectDir}/nextflow.config"
+
+params {
+    variant_caller = "Strelka2"
+    liftover_direction = "GRCh38ToGRCh37"
+}
+
+includeConfig "${projectDir}/test/common.config"
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()