scripts/broad_dsde_workflows/RevertBamToUnmappedRGBamsWf_170107.inputs.json

@@ -1,16 +0,0 @@
-{
-
-  "RevertBamToUnmappedRGBamsWf.ref_fasta": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta",
-  "RevertBamToUnmappedRGBamsWf.ref_fasta_index": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.fai",
-  
-  "RevertBamToUnmappedRGBamsWf.input_bam": "gs://gatk-test-data/wgs_bam/NA12878_20k_b37/NA12878.bam",
-
-  "RevertBamToUnmappedRGBamsWf.output_dir": ".",
-
-  "RevertBamToUnmappedRGBamsWf.RevertBamToUnmappedRGBams.max_discard_pct": 0.01,
-
-  "RevertBamToUnmappedRGBamsWf.RevertBamToUnmappedRGBams.disk_size": 10,
-  "RevertBamToUnmappedRGBamsWf.RevertBamToUnmappedRGBams.mem_size": "1 GB",
-  "RevertBamToUnmappedRGBamsWf.SortBamByQueryname.disk_size": 10,
-  "RevertBamToUnmappedRGBamsWf.SortBamByQueryname.mem_size": "3500 MB"
-}

scripts/broad_dsde_workflows/RevertBamToUnmappedRGBamsWf_170306.inputs.json

@@ -0,0 +1,16 @@
+{
+
+  "RevertBamToUnmappedRGBamsWf.ref_fasta": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta",
+  "RevertBamToUnmappedRGBamsWf.ref_fasta_index": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.fai",
+  
+  "RevertBamToUnmappedRGBamsWf.input_bam": "gs://gatk-test-data/wgs_bam/NA12878_20k_b37/NA12878.bam",
+  "RevertBamToUnmappedRGBamsWf.SplitReadsByRG.input_bam_index": "gs://gatk-test-data/wgs_bam/NA12878_20k_b37/NA12878.bai",
+  
+  "RevertBamToUnmappedRGBamsWf.RevertBamToUnmapped.max_discard_pct": 0.01,
+
+  "RevertBamToUnmappedRGBamsWf.SplitReadsByRG.disk_size": "10",
+  "RevertBamToUnmappedRGBamsWf.SplitReadsByRG.mem_size": "1 GB",
+
+  "RevertBamToUnmappedRGBamsWf.RevertBamToUnmapped.disk_size": 10,
+  "RevertBamToUnmappedRGBamsWf.RevertBamToUnmapped.mem_size": "1 GB"
+}

scripts/broad_dsde_workflows/RevertBamToUnmappedRGBamsWf_170107.wdl → scripts/broad_dsde_workflows/RevertBamToUnmappedRGBamsWf_170306.wdl

@@ -26,33 +26,59 @@
 
 # TASK DEFINITIONS
 
-# Revert a BAM to uBAMs, one per readgroup
-task RevertBamToUnmappedRGBams {
+# Split sample BAM into per-readgroup BAMs
+task SplitReadsByRG {
   File input_bam
-  String output_dir
+  File input_bam_index
+  Int disk_size
+  String mem_size
+
+  command {
+    java -Xmx4000m -jar /usr/gitc/GATK4.jar \
+      SplitReads \
+      -I ${input_bam} \
+      -O . \
+      -RG 
+  }
+  runtime {
+    docker: "broadinstitute/genomes-in-the-cloud:2.2.5-1486412288"
+    disks: "local-disk " + disk_size + " HDD"
+    memory: mem_size
+  }
+  output {
+    Array[File] readgroup_bams = glob("*.bam")
+  }
+}
+
+# Revert a BAM to uBAM
+task RevertBamToUnmapped {
+  File input_bam
+  String output_basename
   Float? max_discard_pct
   Int disk_size
   String mem_size
 
+  String output_name = "${output_basename}.bam"
+
   command {
-    java -Xmx1000m -jar /usr/gitc/picard.jar \
+    java -Xmx4000m -jar /usr/gitc/picard.jar \
     RevertSam \
     INPUT=${input_bam} \
-    O=${output_dir} \
-    OUTPUT_BY_READGROUP=true \
+    O=${output_name} \
+    OUTPUT_BY_READGROUP=false \
     VALIDATION_STRINGENCY=LENIENT \
     SANITIZE=TRUE \
     MAX_DISCARD_FRACTION=${max_discard_pct} \
     ATTRIBUTE_TO_CLEAR=FT \
     SORT_ORDER=queryname 
   }
   runtime {
-    docker: "broadinstitute/genomes-in-the-cloud:2.2.3-1469027018"
+    docker: "broadinstitute/genomes-in-the-cloud:2.2.5-1486412288"
     disks: "local-disk " + disk_size + " HDD"
     memory: mem_size
   }
   output {
-    Array[File] unmapped_bams = glob("*.bam")
+    File unmapped_bam = "${output_name}"
   }
 }
 
@@ -61,17 +87,28 @@ workflow RevertBamToUnmappedRGBamsWf {
   File input_bam
   File ref_fasta
   File ref_fasta_index
-  String output_dir
 
-  # Revert inputs to unmapped
-  call RevertBamToUnmappedRGBams {
-    input:
-      input_bam = input_bam,
-      output_dir = output_dir
+  # Split input BAM by readgroup
+  call SplitReadsByRG {
+    input: 
+      input_bam = input_bam
+  }
+
+  scatter (readgroup_bam in SplitReadsByRG.readgroup_bams) {
+
+    String sub_strip_path = "gs://.*/"
+    String sub_strip_suffix = ".bam$"
+
+    # Revert readgroup BAMs to unmapped
+    call RevertBamToUnmapped {
+      input:
+        input_bam = readgroup_bam,
+        output_basename = sub(sub(input_bam, sub_strip_path, ""), sub_strip_suffix, "") + ".unmapped"
+    }
   }
 
   # Outputs that will be retained when execution is complete
   output {
-    Array[File] unmapped_bams_output=RevertBamToUnmappedRGBams.unmapped_bams
+    Array[File] unmapped_bams_output=RevertBamToUnmapped.unmapped_bam
   }
 }