Update NFTest sample (#144)

* replace CPCG with HG003 as NFtest sample * replace CPCG with HG003 * Update CHANGELOG.md * Autofix Nextflow configuration regression tests --------- Co-authored-by: Mootor <mmootor@ip-0A125967.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net> Co-authored-by: nwiltsie <[email protected]>
uclahs-cds · May 2, 2024 · 1cf467f · 1cf467f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@ All notable changes to the call-gSV pipeline.
 ## [Unreleased]
 
 ### Changed
+- Use HG003 as test sample for NFTest
 - Update Nextflow configuration test workflows
 
 ---

diff --git a/nftest.yaml b/nftest.yaml
@@ -7,31 +7,31 @@ global:
 
 cases:
   - name: gsv_discovery-all-tools-std-input
-    message: test development branch using all tools and standard paired tumor and normal test input CPCG0196-B1 of a-partial size
+    message: test development branch using all tools and standard paired tumor and normal test input HG003 of 5X depth of coverage
     nf_script: ./main.nf
     nf_config: ./test/config/gsv_discovery-all-tools.config
     params_file: ./test/yaml/gsv_test-std-input.yaml
     skip: false
     verbose: true
     asserts:
-      - actual: call-gSV-*/CPCG0196-B1/DELLY-*/output/DELLY-*_TEST_CPCG0196-B1_gCNV.bcf
-        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/DELLY-1.2.6/DELLY-1.2.6_TEST_CPCG0196-B1_gCNV.bcf
+      - actual: call-gSV-*/HG003/DELLY-*/output/DELLY-*_TEST_HG003_gCNV.bcf
+        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/DELLY-1.2.6/DELLY-1.2.6_TEST_HG003_gCNV.bcf
         script: test/assert_bcf_vcf.sh
 
-      - actual: call-gSV-*/CPCG0196-B1/DELLY-*/output/DELLY-*_TEST_CPCG0196-B1_gSV.bcf
-        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/DELLY-1.2.6/DELLY-1.2.6_TEST_CPCG0196-B1_gSV.bcf
+      - actual: call-gSV-*/HG003/DELLY-*/output/DELLY-*_TEST_HG003_gSV.bcf
+        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/DELLY-1.2.6/DELLY-1.2.6_TEST_HG003_gSV.bcf
         script: test/assert_bcf_vcf.sh
 
-      - actual: call-gSV-*/CPCG0196-B1/Manta-*/output/Manta-*_TEST_CPCG0196-B1_candidateSmallIndels.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/Manta-1.6.0/Manta-1.6.0_TEST_CPCG0196-B1_candidateSmallIndels.vcf.gz
+      - actual: call-gSV-*/HG003/Manta-*/output/Manta-*_TEST_HG003_candidateSmallIndels.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/Manta-1.6.0/Manta-1.6.0_TEST_HG003_candidateSmallIndels.vcf.gz
         script: test/assert_bcf_vcf.sh
 
-      - actual: call-gSV-*/CPCG0196-B1/Manta-*/output/Manta-*_TEST_CPCG0196-B1_candidateSV.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/Manta-1.6.0/Manta-1.6.0_TEST_CPCG0196-B1_candidateSV.vcf.gz
+      - actual: call-gSV-*/HG003/Manta-*/output/Manta-*_TEST_HG003_candidateSV.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/Manta-1.6.0/Manta-1.6.0_TEST_HG003_candidateSV.vcf.gz
         script: test/assert_bcf_vcf.sh
 
-      - actual: call-gSV-*/CPCG0196-B1/Manta-*/output/Manta-*_TEST_CPCG0196-B1_diploidSV.vcf.gz
-        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/Manta-1.6.0/Manta-1.6.0_TEST_CPCG0196-B1_diploidSV.vcf.gz
+      - actual: call-gSV-*/HG003/Manta-*/output/Manta-*_TEST_HG003_diploidSV.vcf.gz
+        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/Manta-1.6.0/Manta-1.6.0_TEST_HG003_diploidSV.vcf.gz
         script: test/assert_bcf_vcf.sh
 
   - name: gsv_discovery-manta-std-input
@@ -55,17 +55,17 @@ cases:
         script: test/assert_bcf_vcf.sh
 
   - name: gsv_discovery-delly-std-input
-    message: test development branch using DELLY and a standard paired tumor and normal test input CPCG0196-B1 of a-partial size
+    message: test development branch using DELLY and a standard paired tumor and normal test input HG003 of a-partial size
     nf_script: ./main.nf
     nf_config: ./test/config/gsv_discovery-delly.config
     params_file: ./test/yaml/gsv_test-std-input.yaml
     skip: false
     verbose: true
     asserts:
-      - actual: call-gSV-*/CPCG0196-B1/DELLY-*/output/DELLY-*_TEST_CPCG0196-B1_gCNV.bcf
-        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/DELLY-1.2.6/DELLY-1.2.6_TEST_CPCG0196-B1_gCNV.bcf
+      - actual: call-gSV-*/HG003/DELLY-*/output/DELLY-*_TEST_HG003_gCNV.bcf
+        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/DELLY-1.2.6/DELLY-1.2.6_TEST_HG003_gCNV.bcf
         script: test/assert_bcf_vcf.sh
 
-      - actual: call-gSV-*/CPCG0196-B1/DELLY-*/output/DELLY-*_TEST_CPCG0196-B1_gSV.bcf
-        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/CPCG0196-B1/DELLY-1.2.6/DELLY-1.2.6_TEST_CPCG0196-B1_gSV.bcf
+      - actual: call-gSV-*/HG003/DELLY-*/output/DELLY-*_TEST_HG003_gSV.bcf
+        expect: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/test-output/gsv_discovery-all-tools-std-input/HG003/DELLY-1.2.6/DELLY-1.2.6_TEST_HG003_gSV.bcf
         script: test/assert_bcf_vcf.sh
diff --git a/test/configtest-F16.json b/test/configtest-F16.json
@@ -66,7 +66,7 @@
       "input": {
         "BAM": {
           "normal": [
-            "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/CPCG0196-B1-downsampled-a-partial-sorted.bam"
+            "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/BWA-MEM2-2.2.1_GATK-4.2.4.1_0000082_HG003_subsampled_5X_sorted.bam"
           ]
         }
       },
@@ -191,7 +191,7 @@
       "sample_to_process": [
         {
           "id": "8675309",
-          "path": "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/CPCG0196-B1-downsampled-a-partial-sorted.bam",
+          "path": "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/BWA-MEM2-2.2.1_GATK-4.2.4.1_0000082_HG003_subsampled_5X_sorted.bam",
           "sample_type": "normal"
         }
       ],

diff --git a/test/yaml/gsv_test-std-input.yaml b/test/yaml/gsv_test-std-input.yaml
@@ -2,4 +2,4 @@
 input:
   BAM:
     normal:
-      - "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/CPCG0196-B1-downsampled-a-partial-sorted.bam"
+      - "/hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/BWA-MEM2-2.2.1_GATK-4.2.4.1_0000082_HG003_subsampled_5X_sorted.bam"