updated the related wdl and deleted the copy of the wdl

broadinstitute · Nov 20, 2023 · 3533181 · 3533181
1 parent 592d93a
commit 3533181
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diff --git a/wdl/Module07XfBatchEffect.wdl b/wdl/Module07XfBatchEffect.wdl
@@ -472,47 +472,6 @@ task MakeCorrelationMatrices {
   }
 }
 
-
-# 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{