SAM/BAM file validation on a list of file

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2017, GATK workflows 
+Copyright (c) 2017, Broad Institute
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

generic.google-papi.options.json

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+{
+	"read_from_cache":false,
+	"default_runtime_attributes": {
+		"zones": "us-central1-a us-central1-b us-central1-c us-central1-f"
+	}
+}

validate-bam.inputs.json

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+{
+  "ValidateBamsWf.bam_list": [ 
+  	"gs://gatk-test-data/wgs_bam/NA12878_24RG_hg38/NA12878_24RG_small.hg38.bam",
+  	"gs://gatk-test-data/wgs_bam/NA12878_24RG_hg38/NA12878_24RG_med.hg38.bam"
+  ],
+
+  "ValidateBamsWf.ValidateBAM.validation_mode": "SUMMARY",
+
+  "ValidateBamsWf.ValidateBAM.mem_size": "1 GB",
+  "ValidateBamsWf.ValidateBAM.disk_size": 100
+}

validate-bam.wdl

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+## Copyright Broad Institute, 2017
+## 
+## This WDL performs format validation on SAM/BAM files in a list
+##
+## Requirements/expectations :
+## - List of SAM or BAM files to validate
+## - Explicit request of either SUMMARY or VERBOSE mode in inputs.json
+##
+## Outputs:
+## - Set of .txt files containing the validation reports, one per input file
+##
+## Cromwell version support 
+## - Successfully tested on v24 and v29
+## - Does not work on versions < v23 due to output syntax
+##
+## Runtime parameters are optimized for Broad's Google Cloud Platform implementation. 
+## For program versions, see docker containers. 
+##
+## LICENSING : 
+## This script is released under the WDL source code license (BSD-3) (see LICENSE in 
+## https://github.com/broadinstitute/wdl). Note however that the programs it calls may 
+## be subject to different licenses. Users are responsible for checking that they are
+## authorized to run all programs before running this script. Please see the docker 
+## page at https://hub.docker.com/r/broadinstitute/genomes-in-the-cloud/ for detailed
+## licensing information pertaining to the included programs.
+
+# WORKFLOW DEFINITION
+workflow ValidateBamsWf {
+  Array[File] bam_list
+
+  # Process the input files in parallel
+  scatter (input_bam in bam_list) {
+
+    # Get the basename, i.e. strip the filepath and the extension
+    String bam_basename = basename(input_bam, ".bam")
+
+    # Run the validation 
+    call ValidateBAM {
+      input:
+        bam_file = input_bam,
+        output_basename = bam_basename + ".validation"
+    }
+  }
+
+  # Outputs that will be retained when execution is complete
+  output {
+    Array[File] validation_reports = ValidateBAM.validation_report
+  }
+}
+
+# TASK DEFINITIONS
+
+# Validate a SAM or BAM using Picard ValidateSamFile
+task ValidateBAM {
+  File bam_file
+  String output_basename
+  String validation_mode 
+  Int disk_size
+  String mem_size
+
+  String output_name = "${output_basename}_${validation_mode}.txt"
+
+  command {
+    java -Xmx3000m -jar /usr/gitc/picard.jar \
+      ValidateSamFile \
+      I=${bam_file} \
+      OUTPUT=${output_name} \
+      MODE=${validation_mode}
+  }
+  runtime {
+    docker: "broadinstitute/genomes-in-the-cloud:2.2.3-1469027018"
+    memory: mem_size
+    cpu: "1"
+    disks: "local-disk " + disk_size + " HDD"
+  }
+  output {
+    File validation_report = "${output_name}"
+  }
+}