diff --git a/wdl/XfBatchEffect.wdl b/wdl/XfBatchEffect.wdl
deleted file mode 100644
index 810c049ea..000000000
--- a/wdl/XfBatchEffect.wdl
+++ /dev/null
@@ -1,674 +0,0 @@
-version 1.0
-
-import "prune_add_af.wdl" as calcAF
-import "batch_effect_helper.wdl" as helper
-import "TasksMakeCohortVcf.wdl" as MiniTasks
-
-workflow XfBatchEffect {
-  input{
-    File vcf
-    File vcf_idx
-    File sample_batch_assignments
-    File batches_list
-    File sample_pop_assignments
-    File excludesamples_list #empty file if need be
-    File famfile
-    File contiglist
-    File? par_bed
-    Int variants_per_shard
-    Int? pairwise_cutoff=2
-    Int? onevsall_cutoff=2
-    String prefix
-    File af_pcrmins_premingq
-    String sv_pipeline_docker
-
-    RuntimeAttr? runtime_attr_merge_labeled_vcfs
-  }
-    Array[String] batches = read_lines(batches_list)
-    Array[Array[String]] contigs = read_tsv(contiglist)
-    
-  # Shard VCF per batch, compute pops-specific AFs, and convert to table of VID & AF stats
-  scatter ( batch in batches ) {
-    # Get list of samples to include & exclude per batch
-    call GetBatchSamplesList {
-      input:
-        vcf=vcf,
-        vcf_idx=vcf_idx,
-        batch=batch,
-        sample_batch_assignments=sample_batch_assignments,
-        probands_list=excludesamples_list,
-        sv_pipeline_docker=sv_pipeline_docker
-    }
-    # Prune VCF to samples 
-    call calcAF.prune_and_add_vafs as getAFs {
-      input:
-        vcf=vcf,
-        vcf_idx=vcf_idx,
-        prefix=batch,
-        sample_pop_assignments=sample_pop_assignments,
-        prune_list=GetBatchSamplesList.exclude_samples_list,
-        famfile=famfile,
-        sv_per_shard=25000,
-        contiglist=contiglist,
-        drop_empty_records="FALSE",
-        par_bed=par_bed,
-        sv_pipeline_docker=sv_pipeline_docker
-    }
-    # Get minimal table of AF data per batch, split by ancestry
-    call GetFreqTable {
-      input:
-        vcf=getAFs.output_vcf,
-        prefix=batch,
-        sv_pipeline_docker=sv_pipeline_docker
-    }
-  }
-
-  # Merge frequency results per batch into a single table of all variants with AF data across batches
-  call MergeFreqTables {
-    input:
-      tables=GetFreqTable.freq_data,
-      batches_list=batches_list,
-      prefix=prefix,
-      sv_pipeline_docker=sv_pipeline_docker
-  }
-  call MergeFreqTables as MergeFreqTables_allPops {
-    input:
-      tables=GetFreqTable.freq_data_allPops,
-      batches_list=batches_list,
-      prefix=prefix,
-      sv_pipeline_docker=sv_pipeline_docker
-  }
-
-  # Compare frequencies before and after minGQ, and generate list of variants
-  # that are significantly different between the steps
-  call CompareFreqsPrePostMinGQPcrminus {
-    input:
-      af_pcrmins_premingq=af_pcrmins_premingq,
-      AF_postMinGQ_table=MergeFreqTables_allPops.merged_table,
-      prefix=prefix,
-      sv_pipeline_docker=sv_pipeline_docker
-  }
-
-  # Generate matrix of correlation coefficients for all batches, by population & SVTYPE
-  #scatter ( pop in populations ) {
-  #  call MakeCorrelationMatrices {
-  #    input:
-  #      freq_table=MergeFreqTables.merged_table,
-  #      pop=pop,
-  #      batches_list=batches_list,
-  #      prefix=prefix,
-  #      sv_pipeline_docker=sv_pipeline_docker
-  #  }
-  #}
-
-  # Make list of nonredundant pairs of batches to be evaluated
-  call MakeBatchPairsList {
-    input:
-      batches_list=batches_list,
-      prefix=prefix,
-      sv_pipeline_docker=sv_pipeline_docker
-  }
-  Array[Array[String]] batch_pairs = read_tsv(MakeBatchPairsList.batch_pairs_list)
-
-  # Compute AF stats per pair of batches & determine variants with batch effects
-  scatter ( pair in batch_pairs ) {
-    call helper.check_batch_effects as check_batch_effects {
-      input:
-        freq_table=MergeFreqTables.merged_table,
-        batch1=pair[0],
-        batch2=pair[1],
-        prefix=prefix,
-        variants_per_shard=variants_per_shard,
-        sv_pipeline_docker=sv_pipeline_docker
-    }
-  }
-  # Collect results from pairwise batch effect detection
-  call MergeVariantFailureLists as merge_pairwise_checks {
-    input:
-      fail_variant_lists=check_batch_effects.batch_effect_variants,
-      prefix="~{prefix}.pairwise_comparisons",
-      sv_pipeline_docker=sv_pipeline_docker
-  }
-
-  # Perform one-vs-all comparison of AFs per batch to find batch-specific sites
-  scatter ( batch in batches ) {
-    call helper.check_batch_effects as one_vs_all_comparison {
-      input:
-        freq_table=MergeFreqTables.merged_table,
-        batch1=batch,
-        batch2="ALL_OTHERS",
-        prefix=prefix,
-        variants_per_shard=variants_per_shard,
-        sv_pipeline_docker=sv_pipeline_docker
-    }
-  }
-  # Collect results from pairwise batch effect detection
-  call MergeVariantFailureLists as merge_one_vs_all_checks {
-    input:
-      fail_variant_lists=one_vs_all_comparison.batch_effect_variants,
-      prefix="~{prefix}.one_vs_all_comparisons",
-      sv_pipeline_docker=sv_pipeline_docker
-  }
-
-  # Distill final table of variants to be reclassified
-  call MakeReclassificationTable {
-    input:
-      freq_table=MergeFreqTables.merged_table,
-      pairwise_fails=merge_pairwise_checks.fails_per_variant_all,
-      onevsall_fails=merge_one_vs_all_checks.fails_per_variant_all,
-      prefix=prefix,
-      pairwise_cutoff = pairwise_cutoff,
-      onevsall_cutoff = onevsall_cutoff,
-      sv_pipeline_docker=sv_pipeline_docker
-  }
-
-  # Apply batch effect labels
-  scatter ( contig in contigs ) {
-    call ApplyBatchEffectLabels as apply_labels_perContig {
-      input:
-        vcf=vcf,
-        vcf_idx=vcf_idx,
-        contig=contig[0],
-        reclassification_table=MakeReclassificationTable.reclassification_table,
-        mingq_prePost_pcrminus_fails=CompareFreqsPrePostMinGQPcrminus.pcrminus_fails,
-        prefix="~{prefix}.~{contig[0]}",
-        sv_pipeline_docker=sv_pipeline_docker
-    }
-  }
-  call MiniTasks.ConcatVcfs as merge_labeled_vcfs {
-    input:
-      vcfs=apply_labels_perContig.labeled_vcf,
-      naive=true,
-      outfile_prefix="~{prefix}.batch_effects_labeled_merged",
-      sv_base_mini_docker=sv_pipeline_docker,
-      runtime_attr_override=runtime_attr_merge_labeled_vcfs
-  }
-
-  output {
-    File labeled_vcf = merge_labeled_vcfs.concat_vcf
-    File labeled_vcf_idx = merge_labeled_vcfs.concat_vcf_idx
-  }
-}
-
-
-# Get list of samples to include & exclude per batch
-# Always exclude probands from all batches
-task GetBatchSamplesList {
-  input{
-    File vcf
-    File vcf_idx
-    String batch
-    File sample_batch_assignments
-    File probands_list
-    String sv_pipeline_docker
-    RuntimeAttr? runtime_attr_override
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 4,
-    disk_gb: 50,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    # Get list of all samples present in VCF header
-    tabix -H ~{vcf} | fgrep -v "##" | cut -f10- | sed 's/\t/\n/g' | sort -Vk1,1 \
-    > all_samples.list
-    # Get list of samples in batch
-    fgrep -w ~{batch} ~{sample_batch_assignments} | cut -f1 \
-    | fgrep -wf - all_samples.list \
-    | fgrep -wvf ~{probands_list} \
-    > "~{batch}.samples.list" || true
-    # Get list of samples not in batch
-    fgrep -wv ~{batch} ~{sample_batch_assignments} | cut -f1 \
-    cat - ~{probands_list} | sort -Vk1,1 | uniq \
-    | fgrep -wf - all_samples.list \
-    > "~{batch}.exclude_samples.list" || true
-  >>>
-
-  output {
-    File include_samples_list = "~{batch}.samples.list"
-    File exclude_samples_list = "~{batch}.exclude_samples.list"
-  }
-
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}
-
-
-# Run vcf2bed and subset to just include VID, SVTYPE, SVLEN, _AC, and _AN
-task GetFreqTable {
-  input{
-    File vcf
-    String prefix
-    String sv_pipeline_docker
-    RuntimeAttr? runtime_attr_override
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 4,
-    disk_gb: 50,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    #Run vcf2bed
-    svtk vcf2bed \
-      --info ALL \
-      --no-samples \
-      ~{vcf} "~{prefix}.vcf2bed.bed"
-    ### Create table of freqs by ancestry
-    #Cut to necessary columns
-    idxs=$( sed -n '1p' "~{prefix}.vcf2bed.bed" \
-            | sed 's/\t/\n/g' \
-            | awk -v OFS="\t" '{ print $1, NR }' \
-            | grep -e 'name\|SVLEN\|SVTYPE\|_AC\|_AN' \
-            | fgrep -v "OTH" \
-            | cut -f2 \
-            | paste -s -d\, || true )
-    cut -f"$idxs" "~{prefix}.vcf2bed.bed" \
-    | sed 's/^name/\#VID/g' \
-    | gzip -c \
-    > "~{prefix}.frequencies.preclean.txt.gz"
-    #Clean frequencies
-    /opt/sv-pipeline/scripts/downstream_analysis_and_filtering/clean_frequencies_table.R \
-      "~{prefix}.frequencies.preclean.txt.gz" \
-      "~{prefix}.frequencies.txt"
-    ### Create table of freqs, irrespective of ancestry
-    #Cut to necessary columns
-    idxs=$( sed -n '1p' "~{prefix}.vcf2bed.bed" \
-            | sed 's/\t/\n/g' \
-            | awk -v OFS="\t" '{ if ($1=="name" || $1=="SVLEN" || $1=="SVTYPE" || $1=="AC" || $1=="AN") print NR }' \
-            | paste -s -d\, || true )
-    cut -f"$idxs" "~{prefix}.vcf2bed.bed" \
-    | sed 's/^name/\#VID/g' \
-    | gzip -c \
-    > "~{prefix}.frequencies.allPops.txt.gz"
-  >>>
-
-  output {
-    File freq_data = "~{prefix}.frequencies.txt.gz"
-    File freq_data_allPops = "~{prefix}.frequencies.allPops.txt.gz"
-  }
-
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}
-
-
-# Combine frequency data across batches
-task MergeFreqTables {
-  input{
-    Array[File] tables
-    File batches_list
-    String prefix
-    String sv_pipeline_docker
-    RuntimeAttr? runtime_attr_override
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 16,
-    disk_gb: 100,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    #Get list of batch IDs and batch table paths
-    while read batch; do
-      echo "$batch"
-      find ./ -name "$batch.frequencies*txt.gz"
-    done < ~{batches_list} | paste - - \
-    > input.list
-    #Make sure all input files have the same number of lines
-    while read batch file; do
-      zcat "$file" | wc -l
-    done < input.list > nlines.list
-    nlines=$( sort nlines.list | uniq | wc -l )
-    if [ "$nlines" -gt 1 ]; then
-      echo "AT LEAST ONE INPUT FILE HAS A DIFFERENT NUMBER OF LINES"
-      exit 0
-    fi
-    #Prep files for paste joining
-    echo "PREPPING FILES FOR MERGING"
-    while read batch file; do
-        #Header
-        zcat "$file" | sed -n '1p' | cut -f1-3
-        #Body
-        zcat "$file" | sed '1d' \
-        | sort -Vk1,1 \
-        | cut -f1-3
-    done < <( sed -n '1p' input.list ) \
-    > header.txt
-    while read batch file; do
-      for wrapper in 1; do
-        #Header
-        zcat "$file" | sed -n '1p' \
-        | cut -f4- | sed 's/\t/\n/g' \
-        | awk -v batch="$batch" '{ print $1"."batch }' \
-        | paste -s
-        #Body
-        zcat "$file" | sed '1d' \
-        | sort -Vk1,1 \
-        | cut -f4-
-      done > "$batch.prepped.txt" 
-    done < input.list
-    #Join files with simple paste
-    paste \
-      header.txt \
-      $( awk -v ORS=" " '{ print $1".prepped.txt" }' input.list ) \
-    | gzip -c \
-    > "~{prefix}.merged_AF_table.txt.gz"
-  >>>
-
-  output {
-    File merged_table = "~{prefix}.merged_AF_table.txt.gz"
-  }
-
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}
-
-
-# Compare 
-task CompareFreqsPrePostMinGQPcrminus {
-  input{
-  File af_pcrmins_premingq
-  File AF_postMinGQ_table
-  String prefix
-  String sv_pipeline_docker
-  RuntimeAttr? runtime_attr_override
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 8,
-    disk_gb: 30,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    /opt/sv-pipeline/scripts/downstream_analysis_and_filtering/compare_freqs_pre_post_minGQ.PCRMinus_only.R \
-      ~{af_pcrmins_premingq} \
-      ~{AF_postMinGQ_table} \
-      ./ \
-      "~{prefix}."
-  >>>
-
-  output {
-    File pcrminus_fails = "~{prefix}.PCRMINUS_minGQ_AF_prePost_fails.VIDs.list"
-    File minGQ_prePost_comparison_data = "~{prefix}.minGQ_AF_prePost_comparison.data.txt.gz"
-    File minGQ_prePost_comparison_plot = "~{prefix}.minGQ_AF_prePost_comparison.plot.png"
-  }
-
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}
-
-
-# Calculate & plot cross-batch correlation coefficient matrixes
-task MakeCorrelationMatrices {
-  input{
-    File freq_table
-    String pop
-    File batches_list
-    String prefix
-    String sv_pipeline_docker
-    RuntimeAttr? runtime_attr_override  
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 8,
-    disk_gb: 50,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    /opt/sv-pipeline/scripts/downstream_analysis_and_filtering/correlate_batches_singlePop.R \
-      ~{batches_list} \
-      ~{freq_table} \
-      "~{pop}" \
-      "~{prefix}.~{pop}"
-  >>>
-  output {
-    Array[File] corr_matrixes = glob("~{prefix}.~{pop}.*.R2_matrix.txt")
-    Array[File] heat_maps = glob("~{prefix}.~{pop}.*heatmap*.pdf")
-    Array[File] dot_plots = glob("~{prefix}.~{pop}.*perBatch_R2_sina_plot.pdf")
-  }
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}
-
-
-# Generate list of all pairs of batches to be compared
-task MakeBatchPairsList {
-  input{
-    File batches_list
-    String prefix
-    String sv_pipeline_docker
-    RuntimeAttr? runtime_attr_override
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 4,
-    disk_gb: 10,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    /opt/sv-pipeline/scripts/downstream_analysis_and_filtering/make_batch_pairs_list.R \
-      ~{batches_list} \
-      "~{prefix}.nonredundant_batch_pairs.txt"
-  >>>
-
-  output {
-    File batch_pairs_list = "~{prefix}.nonredundant_batch_pairs.txt"
-  }
-
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}
-
-
-# Merge lists of batch effect checks and count total number of times each variant failed
-task MergeVariantFailureLists {
-  input{
-    Array[File] fail_variant_lists
-    String prefix
-    String sv_pipeline_docker
-    RuntimeAttr? runtime_attr_override
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 4,
-    disk_gb: 10,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    #Write list of paths to all batch effect variant lists
-    #Get master list of PCR+ to PCR+ failures   #removed from the PCR- only projects
-    #Get master list of PCR- to PCR- failures   #removed from the PCR- only projects
-    #Get master list of PCR+ to PCR- failures   #removed from the PCR- only projects
-    #Get master list of all possible failures
-    cat ~{write_lines(fail_variant_lists)} \
-    | xargs -I {} cat {} \
-    | sort -Vk1,1 | uniq -c \
-    | awk -v OFS="\t" '{ print $2, $1 }' \
-    > "~{prefix}.all.failures.txt" || true
-  >>>
-
-  output {
-    File fails_per_variant_all = "~{prefix}.all.failures.txt"
-  }
-
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}
-
-
-# Consolidate all batch effect check results into a single table with reclassification per variant
-task MakeReclassificationTable {
-  input{
-    File freq_table
-    File pairwise_fails
-    File onevsall_fails
-    String prefix
-    Int? pairwise_cutoff
-    Int? onevsall_cutoff
-    String sv_pipeline_docker
-    RuntimeAttr? runtime_attr_override
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 8,
-    disk_gb: 10,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    /opt/sv-pipeline/scripts/downstream_analysis_and_filtering/make_batch_effect_reclassification_table.PCRMinus_only.R \
-      ~{freq_table} \
-      ~{pairwise_fails} \
-      ~{onevsall_fails} \
-      "~{prefix}.batch_effect_reclassification_table.txt" \
-      ~{pairwise_cutoff} \
-      ~{onevsall_cutoff}
-  >>>
-
-  output {
-    File reclassification_table = "~{prefix}.batch_effect_reclassification_table.txt"
-  }
-
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}
-
-
-# Apply batch effect labels to VCF
-task ApplyBatchEffectLabels {
-  input{
-    File vcf
-    File vcf_idx
-    String contig
-    File reclassification_table
-    File mingq_prePost_pcrminus_fails
-    String prefix
-    String sv_pipeline_docker
-    RuntimeAttr? runtime_attr_override
-  }
-  RuntimeAttr default_attr = object {
-    cpu_cores: 1, 
-    mem_gb: 4,
-    disk_gb: 50,
-    boot_disk_gb: 10,
-    preemptible_tries: 3,
-    max_retries: 1
-  }
-  RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
-  command <<<
-    set -euo pipefail
-    tabix -h ~{vcf} ~{contig} \
-    | /opt/sv-pipeline/scripts/downstream_analysis_and_filtering/label_batch_effects.PCRMinus_only.py \
-        --unstable-af-pcrminus ~{mingq_prePost_pcrminus_fails} \
-        stdin \
-        ~{reclassification_table} \
-        stdout \
-        | bgzip -c \
-        > "~{prefix}.batch_effects_labeled.vcf.gz"
-    tabix -p vcf -f "~{prefix}.batch_effects_labeled.vcf.gz"
-  >>>
-
-  output {
-    File labeled_vcf = "~{prefix}.batch_effects_labeled.vcf.gz"
-    File labeled_vcf_idx = "~{prefix}.batch_effects_labeled.vcf.gz.tbi"
-  }
-
-  runtime {
-    cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
-    memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
-    disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
-    bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_docker
-    preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
-    maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
-  }
-}