feat: gzip picard validate STDOUT

.gitignore

@@ -14,6 +14,7 @@
 **/womtool*
 *.jar
 runs/
+out/
 miniwdl_call_cache/
 miniwdl_singularity_cache/
 _LAST
@@ -29,7 +30,7 @@ _LAST
 results*/
 output*/
 
-# Ignore JSONs in the root (probably being used for input to sprocket run)
+# Ignore JSONs in the root (probably being used for input)
 /*.json
 
 # Ignore `sprocket doc` dir

tools/CHANGELOG.md

@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
+## 2026 February
+
+### Changed
+
+- gzip `picard.validate_bam` output when not in `summary_mode` [#298](https://github.com/stjudecloud/workflows/pull/298)
+- Lowered default disk allocation for `picard.validate_bam` [#298](https://github.com/stjudecloud/workflows/pull/298)
+
 ## 2026 January
 
 ### Changed

tools/picard.wdl

@@ -194,14 +194,15 @@ task validate_bam {
         Int modify_disk_size_gb = 0
     }
 
+    String outfile = if summary_mode then outfile_name else outfile_name + ".gz"
     String mode_arg = if (summary_mode) then "--MODE SUMMARY" else ""
     String stringency_arg = (
         if (index_validation_stringency_less_exhaustive)
         then "--INDEX_VALIDATION_STRINGENCY LESS_EXHAUSTIVE"
         else ""
     )
     Float bam_size = size(bam, "GiB")
-    Int disk_size_gb = ceil(bam_size * 2) + 10 + modify_disk_size_gb
+    Int disk_size_gb = ceil(bam_size) + 10 + modify_disk_size_gb
     Int java_heap_size = ceil(memory_gb * 0.9)
 
     command <<<
@@ -217,7 +218,8 @@ task validate_bam {
             --VALIDATION_STRINGENCY "~{validation_stringency}" \
             ~{sep(" ", prefix("--IGNORE ", squote(ignore_list)))} \
             --MAX_OUTPUT ~{max_errors} \
-            > "~{outfile_name}" \
+            ~{if !summary_mode then "| gzip" else ""} \
+            > "~{outfile}" \
             || rc=$?
 
         # rc = 0 = success
@@ -235,16 +237,16 @@ task validate_bam {
         fi
 
         if ! ~{succeed_on_errors} \
-            && [ "$(grep -Ec "$GREP_PATTERN" "~{outfile_name}")" -gt 0 ]
+            && [ "$(grep -Ec "$GREP_PATTERN" "~{outfile}")" -gt 0 ]
         then
             >&2 echo "Problems detected by Picard ValidateSamFile"
-            >&2 grep -E "$GREP_PATTERN" "~{outfile_name}"
+            >&2 grep -E "$GREP_PATTERN" "~{outfile}"
             exit $rc
         fi
     >>>
 
     output {
-        File validate_report = outfile_name
+        File validate_report = outfile
     }
 
     runtime {