From ffd76249a2170e5c4f5422789199a4d4f960c41b Mon Sep 17 00:00:00 2001
From: Steve Huang <shuang@broadinstitute.org>
Date: Mon, 22 Jan 2024 21:07:54 -0500
Subject: [PATCH] make several BAM ops more frugal: [GATK ValidateSamFile,
 samtools fastq, samtools reset]

---
 wdl/tasks/Utility/BAMutils.wdl | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/wdl/tasks/Utility/BAMutils.wdl b/wdl/tasks/Utility/BAMutils.wdl
index 73c7f28f1..36441316f 100644
--- a/wdl/tasks/Utility/BAMutils.wdl
+++ b/wdl/tasks/Utility/BAMutils.wdl
@@ -282,7 +282,6 @@ task ValidateSamFile {
         RuntimeAttr? runtime_attr_override
     }
 
-    Int disk_size = ceil(size(bam, "GiB")) + 50
     String output_basename = basename(basename(bam, ".bam"), ".cram")
     String output_name = "${output_basename}_${validation_mode}.txt"
 
@@ -307,9 +306,12 @@ task ValidateSamFile {
     }
 
     #########################
+
+    Int disk_size = ceil(size(bam, "GiB")) + 10
+
     RuntimeAttr default_attr = object {
         cpu_cores:          2,
-        mem_gb:             8,
+        mem_gb:             6,
         disk_gb:            disk_size,
         preemptible_tries:  2,
         max_retries:        1,
@@ -1280,7 +1282,7 @@ task BamToFastq {
 
     RuntimeAttr default_attr = object {
         cpu_cores:          2,
-        mem_gb:             8,
+        mem_gb:             6,
         disk_gb:            disk_size,
         preemptible_tries:  2,
         max_retries:        1,
@@ -1491,9 +1493,9 @@ task SamtoolsReset {
 
         time gcloud storage cp ~{bam} ~{local_bam}
 
-        samtools view -@1 ~{local_bam} | grep -v "^@" | awk -F '\t' '{print $2}' | sort | uniq -c > orignal.SAM-flag.stats.txt &
+        samtools view ~{local_bam} | grep -v "^@" | awk -F '\t' '{print $2}' | sort | uniq -c > orignal.SAM-flag.stats.txt &
 
-        samtools reset -@3 \
+        samtools reset -@4 \
             --remove-tag ~{sep=',' tags_to_drop} \
             -o ~{prefix}.unaligned.bam \
             ~{local_bam}
@@ -1502,8 +1504,8 @@ task SamtoolsReset {
 
     #########################
     RuntimeAttr default_attr = object {
-        cpu_cores:          4,
-        mem_gb:             16,
+        cpu_cores:          6,
+        mem_gb:             10,
         disk_gb:            disk_size,
         preemptible_tries:  2,
         max_retries:        1,