From 39e2f8f86e06775b61bc2d31392f91ac0cdc42e2 Mon Sep 17 00:00:00 2001
From: "Thomas B. Mooney" <tmooney@genome.wustl.edu>
Date: Thu, 15 Apr 2021 09:11:22 -0500
Subject: [PATCH] Save the BAM/CRAM index and a separate workflow for only
 indexing.

---
 Index.wdl          | 50 ++++++++++++++++++++++++++++++++++++++++++++++
 SingleSampleQc.wdl |  1 +
 2 files changed, 51 insertions(+)
 create mode 100644 Index.wdl

diff --git a/Index.wdl b/Index.wdl
new file mode 100644
index 0000000..ee0a96e
--- /dev/null
+++ b/Index.wdl
@@ -0,0 +1,50 @@
+version 1.0
+
+## Portions Copyright Broad Institute, 2018
+##
+## This WDL pipeline implements QC in human whole-genome or exome/targeted sequencing data.
+##
+## Requirements/expectations
+## - Human paired-end sequencing data in aligned BAM or CRAM format
+## - Input BAM/CRAM files must additionally comply with the following requirements:
+## - - files must pass validation by ValidateSamFile
+## - - reads are provided in query-sorted order
+## - - all reads must have an RG tag
+## - Reference genome must be Hg38 with ALT contigs
+##
+## 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 open source code license (BSD-3).
+## Full license text at https://github.com/openwdl/wdl/blob/master/LICENSE
+## 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.
+## - [Picard](https://broadinstitute.github.io/picard/)
+## - [VerifyBamID2](https://github.com/Griffan/VerifyBamID)
+
+# Git URL import
+import "https://raw.githubusercontent.com/genome/qc-analysis-pipeline/master/tasks/Qc.wdl" as QC
+
+# WORKFLOW DEFINITION
+workflow Index {
+  input {
+    File input_bam
+    String base_name
+    File ref_cache
+    Int preemptible_tries
+  }
+
+  # Generate a BAM or CRAM index
+  call QC.BuildBamIndex as BuildBamIndex {
+    input:
+      input_bam = input_bam,
+      base_name = base_name,
+      ref_cache = ref_cache,
+      preemptible_tries = preemptible_tries
+  }
+
+  output {
+    File bam_index = BuildBamIndex.bam_index
+  }
+}
diff --git a/SingleSampleQc.wdl b/SingleSampleQc.wdl
index 8a4a17e..a71d686 100644
--- a/SingleSampleQc.wdl
+++ b/SingleSampleQc.wdl
@@ -187,5 +187,6 @@ workflow SingleSampleQc {
     File? hs_metrics = CollectHsMetrics.metrics
 
     File input_bam_md5 = CalculateChecksum.md5
+    File input_bam_index = BuildBamIndex.bam_index
   }
 }