Migrate CleanVcf into GATK

.github/.dockstore.yml

@@ -141,6 +141,7 @@ workflows:
     filters:
       branches:
         - main
+        - kj_sv_cleanvcf
       tags:
         - /.*/
 

dockerfiles/sv-pipeline/Dockerfile

@@ -70,13 +70,9 @@ RUN plink2 || true
 # -Compile StitchFragmentedCNVs Java program
 # -Compile StitchFragmentedCNVs unit tests
 # -Compile VCFParser unit tests
-# -Compile and test CleanVCFPart1 Java program
-# -Compile and test CleanVCFPart1 unit tests
 ENV STITCH_JAR="/opt/sv-pipeline/java/build/StitchFragmentedCNVs.jar"
 ARG STITCH_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/StitchFragmentedCNVsUnitTest.jar"
 ARG VCF_PARSER_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/VCFParserUnitTest.jar"
-ENV CLEAN_VCF_PART_1_JAR="/opt/sv-pipeline/java/build/CleanVCFPart1.jar"
-ARG CLEAN_VCF_PART_1_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/CleanVCFPart1UnitTest.jar"
 ARG BUILD_DEPS="openjdk-8-jdk"
 ARG DEBIAN_FRONTEND=noninteractive
 RUN export APT_TRANSIENT_PACKAGES=$(diff_of_lists.sh "$BUILD_DEPS" $APT_REQUIRED_PACKAGES) && \
@@ -97,14 +93,6 @@ RUN export APT_TRANSIENT_PACKAGES=$(diff_of_lists.sh "$BUILD_DEPS" $APT_REQUIRED
     echo "Running VCFParserUnitTest..." && \
     java -enableassertions -jar $VCF_PARSER_UNIT_TEST_JAR && \
     rm -rf build/classes/* $VCF_PARSER_UNIT_TEST_JAR && \
-    javac -d build/classes org/broadinstitute/svpipeline/CleanVCFPart1.java org/broadinstitute/svpipeline/VCFParser.java && \
-    jar cfe build/CleanVCFPart1.jar "org.broadinstitute.svpipeline.CleanVCFPart1" -C build/classes . && \
-    rm -rf build/classes/* && \
-    javac -d build/classes org/broadinstitute/svpipeline/CleanVCFPart1UnitTest.java org/broadinstitute/svpipeline/CleanVCFPart1.java org/broadinstitute/svpipeline/VCFParser.java && \
-    jar cfe build/CleanVCFPart1UnitTest.jar "org.broadinstitute.svpipeline.CleanVCFPart1UnitTest" -C build/classes . && \
-    echo "Running CleanVCFPart1UnitTest..." && \
-    java -enableassertions -jar $CLEAN_VCF_PART_1_UNIT_TEST_JAR && \
-    rm -rf build/classes/* $CLEAN_VCF_PART_1_UNIT_TEST_JAR && \
     apt-get -qqy remove --purge $APT_TRANSIENT_PACKAGES && \
     apt-get -qqy autoremove --purge && \
     apt-get -qqy clean && \

inputs/values/dockers.json

@@ -12,8 +12,8 @@
   "samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2024-10-25-v0.29-beta-5ea22a52",
   "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2024-10-25-v0.29-beta-5ea22a52",
   "sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:2024-10-25-v0.29-beta-5ea22a52",
-  "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-11-15-v1.0-488d7cb0",
-  "sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-11-15-v1.0-488d7cb0",
+  "sv_pipeline_docker": "us-central1-docker.pkg.dev/talkowski-training/kj-development/sv-pipeline:kj-clean-vcf-170ec7c38b004f02639b5f82270113b74162fe79",
+  "sv_pipeline_qc_docker": "us-central1-docker.pkg.dev/talkowski-training/kj-development/sv-pipeline:kj-clean-vcf-170ec7c38b004f02639b5f82270113b74162fe79",
   "wham_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/wham:2024-10-25-v0.29-beta-5ea22a52",
   "igv_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
   "duphold_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9",
@@ -28,5 +28,5 @@
   "sv_utils_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-utils:2024-10-25-v0.29-beta-5ea22a52",
   "gq_recalibrator_docker": "us.gcr.io/broad-dsde-methods/markw/gatk:mw-tb-form-sv-filter-training-data-899360a",
   "str": "us.gcr.io/broad-dsde-methods/gatk-sv/str:2023-05-23-v0.27.3-beta-e537bdd6",
-  "denovo": "us.gcr.io/broad-dsde-methods/gatk-sv/denovo:2024-11-15-v1.0-488d7cb0"
+  "denovo": "us-central1-docker.pkg.dev/talkowski-training/kj-development/denovo:kj-clean-vcf-170ec7c38b004f02639b5f82270113b74162fe79"
 }