Second round of MakeCohortVcf updates from gnomAD (#288)

dockerfiles/sv-pipeline-base/Dockerfile

@@ -49,7 +49,7 @@ ARG CONDA_DEP_TRANSIENT="make git wget"
 ARG CONDA_DEP="software-properties-common zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libssl-dev libblas-dev liblapack-dev libatlas-base-dev g++ gfortran ${CONDA_DEP_TRANSIENT}"
 # versions of bedtools > 2.27.0 seem to have lost the ability to read gzipped files
 # pandas 1.0.0 causes problem with bedtools in aggregate.py
-ARG PYTHON_PKGS="setuptools=52.0.0 wheel=0.34.2 bzip2=1.0.8 cython=0.29.14 numpy=1.18.1 pandas=0.25.3 scikit-learn=0.22.1 scipy=1.4.1 intervaltree=3.0.2 matplotlib=3.1.3 natsort=7.0.1 bedtools=2.27.0 pybedtools=0.8.1 pysam=0.14.1=py36_htslib1.7_0"
+ARG PYTHON_PKGS="pip=21.2.2 setuptools=52.0.0 wheel=0.34.2 bzip2=1.0.8 cython=0.29.14 numpy=1.18.1 pandas=0.25.3 scikit-learn=0.22.1 scipy=1.4.1 intervaltree=3.0.2 matplotlib=3.1.3 natsort=7.0.1 bedtools=2.27.0 pybedtools=0.8.1 pysam=0.14.1=py36_htslib1.7_0"
 ENV LANG=C.UTF-8
 ENV LC_ALL=C.UTF-8
 ARG CONDA_INSTALL_DIR="/opt/conda"

dockerfiles/sv-pipeline-hail/Dockerfile

@@ -0,0 +1,9 @@
+# GATK SV Pipeline Hail dockerfile
+
+# IMPORTANT: these arguments must be specified at the begining to take advantage of multi-stage build AND runtime specification of base images
+ARG SV_PIPELINE_IMAGE=gatksv/sv-pipeline:latest
+FROM ${SV_PIPELINE_IMAGE}
+
+# Dependencies for creating a Hail cluster on GCS DataProc
+RUN pip3 --no-cache-dir install hail==0.2.71 && \
+    pip3 --no-cache-dir install google-cloud-dataproc \

dockerfiles/sv-pipeline/Dockerfile

@@ -48,3 +48,51 @@ RUN apt-get -qqy update --fix-missing && \
            /usr/share/man/?? \
            /usr/share/man/??_*
 ENV PATH="/opt/:${PATH}"
+
+# Compile StitchFragmentedCNVs Java program
+ENV STITCH_JAR="/opt/sv-pipeline/java/build/StitchFragmentedCNVs.jar"
+RUN cd /opt/sv-pipeline/java && \
+    mkdir -p build/classes && \
+    javac -d build/classes org/broadinstitute/svpipeline/StitchFragmentedCNVs.java org/broadinstitute/svpipeline/VCFParser.java && \
+    jar cfe build/StitchFragmentedCNVs.jar "org.broadinstitute.svpipeline.StitchFragmentedCNVs" -C build/classes . && \
+    rm -r build/classes
+
+# Compile StitchFragmentedCNVs unit tests
+ENV STITCH_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/StitchFragmentedCNVsUnitTest.jar"
+RUN cd /opt/sv-pipeline/java && \
+    mkdir -p build/classes && \
+    javac -d build/classes org/broadinstitute/svpipeline/StitchFragmentedCNVsUnitTest.java org/broadinstitute/svpipeline/StitchFragmentedCNVs.java org/broadinstitute/svpipeline/VCFParser.java && \
+    jar cfe build/StitchFragmentedCNVsUnitTest.jar "org.broadinstitute.svpipeline.StitchFragmentedCNVsUnitTest" -C build/classes . && \
+    echo "Running StitchFragmentedCNVsUnitTest..." && \
+    java -enableassertions -jar $STITCH_UNIT_TEST_JAR && \
+    rm -r build/classes $STITCH_UNIT_TEST_JAR
+
+# Compile VCFParser unit tests
+ENV VCF_PARSER_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/VCFParserUnitTest.jar"
+RUN cd /opt/sv-pipeline/java && \
+    mkdir -p build/classes && \
+    javac -d build/classes org/broadinstitute/svpipeline/VCFParserUnitTest.java org/broadinstitute/svpipeline/VCFParser.java && \
+    jar cfe build/VCFParserUnitTest.jar "org.broadinstitute.svpipeline.VCFParserUnitTest" -C build/classes . && \
+    echo "Running VCFParserUnitTest..." && \
+    java -enableassertions -jar $VCF_PARSER_UNIT_TEST_JAR && \
+    rm -r build/classes $VCF_PARSER_UNIT_TEST_JAR
+
+# Compile and test CleanVCFPart1 Java program
+ENV CLEAN_VCF_PART_1_JAR="/opt/sv-pipeline/java/build/CleanVCFPart1.jar"
+RUN cd /opt/sv-pipeline/java && \
+    mkdir -p build/classes && \
+    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 -r build/classes
+
+# Compile and test CleanVCFPart1 unit tests
+ENV CLEAN_VCF_PART_1_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/CleanVCFPart1UnitTest.jar"
+RUN cd /opt/sv-pipeline/java && \
+    mkdir -p 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 -r build/classes $CLEAN_VCF_PART_1_UNIT_TEST_JAR && \
+    rm -rf /tmp/* /var/tmp/*
+

input_templates/GATKSVPipelineBatch.ref_panel_1kg.json.tmpl

@@ -28,6 +28,8 @@
   "GATKSVPipelineBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GATKSVPipelineBatch.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
+  "GATKSVPipelineBatch.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},
+  "GATKSVPipelineBatch.sv_pipeline_updates_docker": {{ dockers.sv_pipeline_updates_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GATKSVPipelineBatch.samtools_cloud_docker": {{ dockers.samtools_cloud_docker | tojson }},
@@ -117,6 +119,9 @@
   "GATKSVPipelineBatch.RegenotypeCNVs.n_RdTest_bins": "100000",
   "GATKSVPipelineBatch.RegenotypeCNVs.n_per_split": "5000",
 
+  "GATKSVPipelineBatch.MakeCohortVcf.chr_x": {{ reference_resources.chr_x | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.chr_y": {{ reference_resources.chr_y | tojson }},
+
   "GATKSVPipelineBatch.MakeCohortVcf.bin_exclude": {{ reference_resources.bin_exclude | tojson }},
   "GATKSVPipelineBatch.MakeCohortVcf.empty_file" : {{ reference_resources.empty_file | tojson }},
   "GATKSVPipelineBatch.MakeCohortVcf.cytobands": {{ reference_resources.cytobands | tojson }},
@@ -126,7 +131,9 @@
   "GATKSVPipelineBatch.MakeCohortVcf.min_sr_background_fail_batches": 0.5,
   "GATKSVPipelineBatch.MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
   "GATKSVPipelineBatch.MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,
+  "GATKSVPipelineBatch.MakeCohortVcf.clean_vcf1b_records_per_shard": 10000,
   "GATKSVPipelineBatch.MakeCohortVcf.samples_per_clean_vcf_step2_shard": 100,
+  "GATKSVPipelineBatch.MakeCohortVcf.clean_vcf5_records_per_shard": 5000,
   "GATKSVPipelineBatch.MakeCohortVcf.random_seed": 0,
   "GATKSVPipelineBatch.MakeCohortVcf.max_shard_size_resolve": 500,
 

input_templates/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.json.tmpl

@@ -34,6 +34,8 @@
   "GATKSVPipelineSingleSample.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
+  "GATKSVPipelineSingleSample.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},
+  "GATKSVPipelineSingleSample.sv_pipeline_updates_docker": {{ dockers.sv_pipeline_updates_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GATKSVPipelineSingleSample.wham_docker": {{ dockers.wham_docker | tojson }},
@@ -84,7 +86,9 @@
   "GATKSVPipelineSingleSample.max_shard_size_resolve" : 500,
   "GATKSVPipelineSingleSample.clean_vcf_max_shards_per_chrom_clean_vcf_step1": 200,
   "GATKSVPipelineSingleSample.clean_vcf_min_records_per_shard_clean_vcf_step1": 5000,
+  "GATKSVPipelineSingleSample.clean_vcf1b_records_per_shard": 10000,
   "GATKSVPipelineSingleSample.clean_vcf_samples_per_clean_vcf_step2_shard": 100,
+  "GATKSVPipelineSingleSample.clean_vcf5_records_per_shard": 5000,
   "GATKSVPipelineSingleSample.clean_vcf_random_seed": 0,
   "GATKSVPipelineSingleSample.run_vcf_qc" : false,
 

input_templates/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.no_melt.json.tmpl

@@ -36,6 +36,8 @@
   "GATKSVPipelineSingleSample.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
+  "GATKSVPipelineSingleSample.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},
+  "GATKSVPipelineSingleSample.sv_pipeline_updates_docker": {{ dockers.sv_pipeline_updates_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GATKSVPipelineSingleSample.wham_docker": {{ dockers.wham_docker | tojson }},
@@ -85,8 +87,10 @@
   "GATKSVPipelineSingleSample.max_shard_size_resolve" : 500,
   "GATKSVPipelineSingleSample.clean_vcf_max_shards_per_chrom_clean_vcf_step1": 200,
   "GATKSVPipelineSingleSample.clean_vcf_min_records_per_shard_clean_vcf_step1": 5000,
+  "GATKSVPipelineSingleSample.clean_vcf1b_records_per_shard": 10000,
   "GATKSVPipelineSingleSample.clean_vcf_samples_per_clean_vcf_step2_shard": 100,
   "GATKSVPipelineSingleSample.clean_vcf_random_seed": 0,
+  "GATKSVPipelineSingleSample.clean_vcf5_records_per_shard": 5000,
   "GATKSVPipelineSingleSample.run_vcf_qc" : false,
 
   "GATKSVPipelineSingleSample.protein_coding_gtf" : {{ reference_resources.protein_coding_gtf | tojson }},

input_templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl

@@ -14,19 +14,26 @@
   "MakeCohortVcf.min_sr_background_fail_batches": 0.5,
   "MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
   "MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,
+  "MakeCohortVcf.clean_vcf1b_records_per_shard": 10000,
+  "MakeCohortVcf.clean_vcf5_records_per_shard": 5000,
   "MakeCohortVcf.samples_per_clean_vcf_step2_shard": 100,
   "MakeCohortVcf.random_seed": 0,
   "MakeCohortVcf.max_shard_size_resolve": 500,
 
   "MakeCohortVcf.linux_docker": "${workspace.linux_docker}",
   "MakeCohortVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
+  "MakeCohortVcf.sv_pipeline_hail_docker": "${workspace.sv_pipeline_hail_docker}",
+  "MakeCohortVcf.sv_pipeline_updates_docker": "${workspace.sv_pipeline_updates_docker}",
   "MakeCohortVcf.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "MakeCohortVcf.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
 
   "MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}",
   "MakeCohortVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
+  "MakeCohortVcf.chr_x": "${workspace.chr_x}",
+  "MakeCohortVcf.chr_y": "${workspace.chr_y}",
+
   "MakeCohortVcf.cohort_name": "${this.sample_set_id}",
   "MakeCohortVcf.batches": "${this.sample_set_id}",
   "MakeCohortVcf.ped_file": "${workspace.cohort_ped_file}",

input_templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl

@@ -14,19 +14,26 @@
   "MakeCohortVcf.min_sr_background_fail_batches": 0.5,
   "MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
   "MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,
+  "MakeCohortVcf.clean_vcf1b_records_per_shard": 10000,
+  "MakeCohortVcf.clean_vcf5_records_per_shard": 5000,
   "MakeCohortVcf.samples_per_clean_vcf_step2_shard": 100,
   "MakeCohortVcf.random_seed": 0,
   "MakeCohortVcf.max_shard_size_resolve": 500,
 
   "MakeCohortVcf.linux_docker": "${workspace.linux_docker}",
   "MakeCohortVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
+  "MakeCohortVcf.sv_pipeline_hail_docker": "${workspace.sv_pipeline_hail_docker}",
+  "MakeCohortVcf.sv_pipeline_updates_docker": "${workspace.sv_pipeline_updates_docker}",
   "MakeCohortVcf.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "MakeCohortVcf.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
 
   "MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}",
   "MakeCohortVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
+  "MakeCohortVcf.chr_x": "${workspace.chr_x}",
+  "MakeCohortVcf.chr_y": "${workspace.chr_y}",
+
   "MakeCohortVcf.cohort_name": "${this.sample_set_set_id}",
   "MakeCohortVcf.batches": "${this.sample_sets.sample_set_id}",
   "MakeCohortVcf.ped_file": "${workspace.cohort_ped_file}",

input_templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl

@@ -1,2 +1,2 @@
-workspace:cloud_sdk_docker	cnmops_docker	condense_counts_docker	gatk_docker	gatk_docker_pesr_override	gcnv_gatk_docker	genomes_in_the_cloud_docker	linux_docker	manta_docker	samtools_cloud_docker	sv_base_docker	sv_base_mini_docker	sv_pipeline_base_docker	sv_pipeline_docker	sv_pipeline_qc_docker	sv_pipeline_rdtest_docker	wham_docker	allosome_file	autosome_file	bin_exclude	cnmops_exclude_list	cohort_ped_file	contig_ploidy_priors	copy_number_autosomal_contigs	cytobands	dbsnp_vcf	delly_exclude_intervals_file	depth_exclude_list	empty_file	exclude_intervals_for_gcnv_filter_intervals	external_af_ref_bed	external_af_ref_bed_prefix	genome_file	inclusion_bed	linc_rna_gtf	manta_region_bed	mei_bed	melt_standard_vcf_header	noncoding_bed	pesr_exclude_list	preprocessed_intervals	primary_contigs_fai	primary_contigs_list	promoter_bed	protein_coding_gtf	reference_build	reference_dict	reference_fasta	reference_index	reference_version	rmsk	segdups	seed_cutoffs	unpadded_intervals_file	wgd_scoring_mask	wham_include_list_bed_file
-{{ dockers.cloud_sdk_docker }}	{{ dockers.cnmops_docker }}	{{ dockers.condense_counts_docker }}	{{ dockers.gatk_docker }}	{{ dockers.gatk_docker_pesr_override }}	{{ dockers.gatk_docker }}	{{ dockers.genomes_in_the_cloud_docker }}	{{ dockers.linux_docker }}	{{ dockers.manta_docker }}	{{ dockers.samtools_cloud_docker }}	{{ dockers.sv_base_docker }}	{{ dockers.sv_base_mini_docker }}	{{ dockers.sv_pipeline_base_docker }}	{{ dockers.sv_pipeline_docker }}	{{ dockers.sv_pipeline_qc_docker }}	{{ dockers.sv_pipeline_rdtest_docker }}	{{ dockers.wham_docker }}	{{ reference_resources.allosome_file }}	{{ reference_resources.autosome_file }}	{{ reference_resources.bin_exclude }}	{{ reference_resources.cnmops_exclude_list }}	gs://broad-dsde-methods-eph/ped_1kgp_all.ped	{{ reference_resources.contig_ploidy_priors }}	{{ reference_resources.copy_number_autosomal_contigs }}	{{ reference_resources.cytobands }}	{{ reference_resources.dbsnp_vcf }}	{{ reference_resources.delly_exclude_intervals_file }}	{{ reference_resources.depth_exclude_list }}	{{ reference_resources.empty_file }}	{{ reference_resources.exclude_intervals_for_gcnv_filter_intervals }}	{{ reference_resources.external_af_ref_bed | tojson }}	{{ reference_resources.external_af_ref_bed_prefix | tojson }}	{{ reference_resources.genome_file }}	{{ reference_resources.inclusion_bed }}	{{ reference_resources.linc_rna_gtf | tojson }}	{{ reference_resources.manta_region_bed }}	{{ reference_resources.mei_bed }}	{{ reference_resources.melt_std_vcf_header }}	{{ reference_resources.noncoding_bed | tojson }}	{{ reference_resources.pesr_exclude_list }}	{{ reference_resources.preprocessed_intervals }}	{{ reference_resources.primary_contigs_fai }}	{{ reference_resources.primary_contigs_list }}	{{ reference_resources.promoter_bed | tojson }}	{{ reference_resources.protein_coding_gtf | tojson }}	{{ reference_resources.reference_build }}	{{ reference_resources.reference_dict }}	{{ reference_resources.reference_fasta }}	{{ reference_resources.reference_index }}	{{ reference_resources.reference_version }}	{{ reference_resources.rmsk }}	{{ reference_resources.segdups }}	{{ reference_resources.seed_cutoffs }}	{{ reference_resources.unpadded_intervals_file }}	{{ reference_resources.wgd_scoring_mask }}	{{ reference_resources.wham_include_list_bed_file }}
+workspace:cloud_sdk_docker	cnmops_docker	condense_counts_docker	gatk_docker	gatk_docker_pesr_override	gcnv_gatk_docker	genomes_in_the_cloud_docker	linux_docker	manta_docker	samtools_cloud_docker	sv_base_docker	sv_base_mini_docker	sv_pipeline_base_docker	sv_pipeline_docker  sv_pipeline_hail_docker  sv_pipeline_updates_docker	sv_pipeline_qc_docker	sv_pipeline_rdtest_docker	wham_docker	allosome_file	autosome_file	bin_exclude	cnmops_exclude_list	cohort_ped_file	contig_ploidy_priors	copy_number_autosomal_contigs	cytobands	dbsnp_vcf	delly_exclude_intervals_file	depth_exclude_list	empty_file	exclude_intervals_for_gcnv_filter_intervals	external_af_ref_bed	external_af_ref_bed_prefix	genome_file	inclusion_bed	linc_rna_gtf	manta_region_bed	mei_bed	melt_standard_vcf_header	noncoding_bed	pesr_exclude_list	preprocessed_intervals	primary_contigs_fai	primary_contigs_list	promoter_bed	protein_coding_gtf	reference_build	reference_dict	reference_fasta	reference_index	reference_version	rmsk	segdups	seed_cutoffs	unpadded_intervals_file	wgd_scoring_mask	wham_include_list_bed_file  chr_x   chr_y
+{{ dockers.cloud_sdk_docker }}	{{ dockers.cnmops_docker }}	{{ dockers.condense_counts_docker }}	{{ dockers.gatk_docker }}	{{ dockers.gatk_docker_pesr_override }}	{{ dockers.gatk_docker }}	{{ dockers.genomes_in_the_cloud_docker }}	{{ dockers.linux_docker }}	{{ dockers.manta_docker }}	{{ dockers.samtools_cloud_docker }}	{{ dockers.sv_base_docker }}	{{ dockers.sv_base_mini_docker }}	{{ dockers.sv_pipeline_base_docker }}	{{ dockers.sv_pipeline_docker }}    {{ dockers.sv_pipeline_hail_docker }}    {{ dockers.sv_pipeline_updates_docker }}	{{ dockers.sv_pipeline_qc_docker }}	{{ dockers.sv_pipeline_rdtest_docker }}	{{ dockers.wham_docker }}	{{ reference_resources.allosome_file }}	{{ reference_resources.autosome_file }}	{{ reference_resources.bin_exclude }}	{{ reference_resources.cnmops_exclude_list }}	gs://broad-dsde-methods-eph/ped_1kgp_all.ped	{{ reference_resources.contig_ploidy_priors }}	{{ reference_resources.copy_number_autosomal_contigs }}	{{ reference_resources.cytobands }}	{{ reference_resources.dbsnp_vcf }}	{{ reference_resources.delly_exclude_intervals_file }}	{{ reference_resources.depth_exclude_list }}	{{ reference_resources.empty_file }}	{{ reference_resources.exclude_intervals_for_gcnv_filter_intervals }}	{{ reference_resources.external_af_ref_bed | tojson }}	{{ reference_resources.external_af_ref_bed_prefix | tojson }}	{{ reference_resources.genome_file }}	{{ reference_resources.inclusion_bed }}	{{ reference_resources.linc_rna_gtf | tojson }}	{{ reference_resources.manta_region_bed }}	{{ reference_resources.mei_bed }}	{{ reference_resources.melt_std_vcf_header }}	{{ reference_resources.noncoding_bed | tojson }}	{{ reference_resources.pesr_exclude_list }}	{{ reference_resources.preprocessed_intervals }}	{{ reference_resources.primary_contigs_fai }}	{{ reference_resources.primary_contigs_list }}	{{ reference_resources.promoter_bed | tojson }}	{{ reference_resources.protein_coding_gtf | tojson }}	{{ reference_resources.reference_build }}	{{ reference_resources.reference_dict }}	{{ reference_resources.reference_fasta }}	{{ reference_resources.reference_index }}	{{ reference_resources.reference_version }}	{{ reference_resources.rmsk }}	{{ reference_resources.segdups }}	{{ reference_resources.seed_cutoffs }}	{{ reference_resources.unpadded_intervals_file }}	{{ reference_resources.wgd_scoring_mask }}	{{ reference_resources.wham_include_list_bed_file }}    {{ reference_resources.chr_x }} {{ reference_resources.chr_y }}