From 0fa1053af22272c197c282e5525cda9d5e6f4048 Mon Sep 17 00:00:00 2001
From: Jason Walker <jwalker@genome.wustl.edu>
Date: Fri, 22 Sep 2017 11:25:33 -0500
Subject: [PATCH] CWL changes to support piping of Picard SamToFastq into
 BWA-MEM as interleaved FASTQ.

---
 unaligned_bam_to_bqsr/align.cwl         | 10 +---------
 unaligned_bam_to_bqsr/align_and_tag.cwl | 16 ++++++----------
 2 files changed, 7 insertions(+), 19 deletions(-)

diff --git a/unaligned_bam_to_bqsr/align.cwl b/unaligned_bam_to_bqsr/align.cwl
index c7ee4f523..47be323f5 100644
--- a/unaligned_bam_to_bqsr/align.cwl
+++ b/unaligned_bam_to_bqsr/align.cwl
@@ -19,19 +19,11 @@ outputs:
         type: File
         outputSource: align_and_tag/aligned_bam
 steps:
-    revert_to_fastq:
-        run: revert_to_fastq.cwl
-        in:
-            bam: bam
-        out:
-            [fastq, second_end_fastq]
     align_and_tag:
         run: align_and_tag.cwl
         in:
-        in:
+            bam: bam
             readgroup: readgroup
             reference: reference
-            fastq: revert_to_fastq/fastq
-            fastq2: revert_to_fastq/second_end_fastq
         out:
             [aligned_bam]
diff --git a/unaligned_bam_to_bqsr/align_and_tag.cwl b/unaligned_bam_to_bqsr/align_and_tag.cwl
index e43893e44..4d0cc4220 100644
--- a/unaligned_bam_to_bqsr/align_and_tag.cwl
+++ b/unaligned_bam_to_bqsr/align_and_tag.cwl
@@ -11,25 +11,21 @@ requirements:
       ramMin: 16000
 stdout: "refAlign.bam"
 arguments:
-    - position: 5
+    - position: 4
       valueFrom: $(runtime.cores)
 inputs:
-    readgroup:
-        type: string
+    bam:
+        type: File
         inputBinding:
             position: 1
-    reference:
+    readgroup:
         type: string
         inputBinding:
             position: 2
-    fastq:
-        type: File
+    reference:
+        type: string
         inputBinding:
             position: 3
-    fastq2:
-        type: File
-        inputBinding:
-            position: 4
 outputs:
     aligned_bam:
             type: stdout