From 38baee980a926e75b7d9911ed2b1f0ee3fc36ad0 Mon Sep 17 00:00:00 2001
From: Jonn Smith <jonn@broadinstitute.org>
Date: Tue, 10 Dec 2024 08:26:30 -0500
Subject: [PATCH] Changed how SRUtils.BamToFq operates.

- Now BamToFq sorts and converts in 2 separate commands.
- Now BamToFq utilizes all available processors.
- Set BamToFq number of processors and ram to 8 and 24 respectively.
---
 wdl/tasks/Utility/SRUtils.wdl | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/wdl/tasks/Utility/SRUtils.wdl b/wdl/tasks/Utility/SRUtils.wdl
index 995221742..235d1ec6a 100644
--- a/wdl/tasks/Utility/SRUtils.wdl
+++ b/wdl/tasks/Utility/SRUtils.wdl
@@ -18,18 +18,33 @@ task BamToFq {
 
     String ref_arg = if defined(reference_fasta) then " --reference " else ""
 
-    Int disk_size = 1 + 4*ceil(size(bam, "GB"))
+    Int disk_size = 1 + 20*ceil(size(bam, "GB"))
 
     command <<<
+
+        # Make sure we use all our proocesors:
+        np=$(cat /proc/cpuinfo | grep ^processor | tail -n1 | awk '{print $NF+1}')
+        if [[ ${np} -gt 2 ]] ; then
+            np=$((np-1))
+        fi
+
         set -euxo pipefail
 
-        samtools sort -n ~{ref_arg} ~{reference_fasta} ~{bam} | samtools bam2fq -@2 \
+        # Have samtools sort use all but one of our processors:
+        # NOTE: the `@` options is for ADDITIONAL threads, not the total number of threads.
+        samtools sort -@$((np-1)) -n ~{ref_arg} ~{reference_fasta} ~{bam} -O bam -o tmp.bam
+        
+        # Have samtools bam2fq use all but one of our processors:
+        # NOTE: the `@` options is for ADDITIONAL threads, not the total number of threads.
+        samtools bam2fq -@$((np-1)) \
             -n \
             -s /dev/null \
+            -c 2 \
             ~{ref_arg} ~{reference_fasta} \
             -1 ~{prefix}.end1.fq.gz \
             -2 ~{prefix}.end2.fq.gz \
-            -0 ~{prefix}.unpaired.fq.gz
+            -0 ~{prefix}.unpaired.fq.gz \
+            tmp.bam
     >>>
 
     output {
@@ -40,8 +55,8 @@ task BamToFq {
 
     #########################
     RuntimeAttr default_attr = object {
-        cpu_cores:          4,
-        mem_gb:             32,
+        cpu_cores:          8,
+        mem_gb:             24,
         disk_gb:            disk_size,
         boot_disk_gb:       25,
         preemptible_tries:  1,