chore: GiB -> GB (#302)

Currently, we compute file sizes in `GiB`. We then use those to request
disk space, but in `GB`. This is silently undercounting the amount of
disk space we need for these tasks. `GB` was chosen to be the common
unit because our variables already end in `_gb` so this is the least
disruptive change.

Before submitting this PR, please make sure:

- [x] You have added a few sentences describing the PR here.
- [ ] The code passes all CI tests without any errors or warnings.
- [ ] You have added tests (when appropriate).
- [x] You have added an entry in any relevant CHANGELOGs (when
appropriate).
- [ ] If you have made any changes to the `scripts/` or `docker/`
directories, please ensure any image versions have been incremented
accordingly!
- [ ] You have updated the README or other documentation to account for
these changes (when appropriate).

Author: adthrasher

data_structures/CHANGELOG.md

@@ -4,6 +4,12 @@ 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
+
+- Converted size checks to GB from GiB [#302](https://github.com/stjudecloud/workflows/pull/302)
+
 ## 2025 September
 
 ### Added

data_structures/read_group.wdl

@@ -123,7 +123,7 @@ task get_read_groups {
         Int modify_disk_size_gb = 0
     }
 
-    Float bam_size = size(bam, "GiB")
+    Float bam_size = size(bam, "GB")
     Int disk_size_gb = ceil(bam_size) + 10 + modify_disk_size_gb
 
     command <<<

template/task-examples.wdl

@@ -44,7 +44,7 @@ task dynamic_disk_and_ram_task {
         Int modify_disk_size_gb = 0
     }
 
-    Int input_size_gb = ceil(size(<input files>, "GiB"))
+    Int input_size_gb = ceil(size(<input files>, "GB"))
 
     Int memory_gb = ceil(input_size_gb * X) + modify_memory_gb
     Int disk_size_gb = ceil(input_size_gb * Y) + modify_disk_size_gb

tools/CHANGELOG.md

@@ -10,6 +10,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/).
 
 - 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)
+- Converted size checks to GB from GiB [#302](https://github.com/stjudecloud/workflows/pull/302)
 
 ## 2026 January
 

tools/arriba.wdl

@@ -175,10 +175,10 @@ task arriba {
         Int modify_disk_size_gb = 0
     }
 
-    Int bam_size_gb = ceil(size(bam, "GiB"))
+    Int bam_size_gb = ceil(size(bam, "GB"))
     Int disk_size_gb = bam_size_gb
-        + ceil(size(gtf, "GiB"))
-        + ceil(size(reference_fasta_gz, "GiB"))
+        + ceil(size(gtf, "GB"))
+        + ceil(size(reference_fasta_gz, "GB"))
         + modify_disk_size_gb
     Int memory_gb = bam_size_gb + modify_memory_gb
 
@@ -273,9 +273,9 @@ task arriba_tsv_to_vcf {
         Int modify_disk_size_gb = 0
     }
 
-    Int input_size_gb = ceil(size(fusions, "GiB"))
+    Int input_size_gb = ceil(size(fusions, "GB"))
     Int disk_size_gb = ceil(input_size_gb)
-        + (ceil(size(reference_fasta, "GiB")) * 3)
+        + (ceil(size(reference_fasta, "GB")) * 3)
         + modify_disk_size_gb
 
     command <<<
@@ -329,7 +329,7 @@ task arriba_extract_fusion_supporting_alignments {
         Int modify_disk_size_gb = 0
     }
 
-    Int input_size_gb = ceil(size(bam, "GiB"))
+    Int input_size_gb = ceil(size(bam, "GB"))
     Int disk_size_gb = ceil(input_size_gb) + 5 + modify_disk_size_gb
 
     command <<<
@@ -374,7 +374,7 @@ task arriba_annotate_exon_numbers {
         Int modify_disk_size_gb = 0
     }
 
-    Int input_size_gb = ceil(size(gtf, "GiB"))
+    Int input_size_gb = ceil(size(gtf, "GB"))
     Int disk_size_gb = ceil(input_size_gb) + 5 + modify_disk_size_gb
 
     command <<<

tools/bwa.wdl

@@ -48,8 +48,8 @@ task bwa_aln {
 
     String output_bam = prefix + ".bam"
 
-    Float input_fastq_size = size(fastq, "GiB")
-    Float reference_size = size(bwa_db_tar_gz, "GiB")
+    Float input_fastq_size = size(fastq, "GB")
+    Float reference_size = size(bwa_db_tar_gz, "GB")
     Int disk_size_gb = (
         ceil((input_fastq_size + reference_size) * 2) + 10 + modify_disk_size_gb
     )
@@ -145,9 +145,9 @@ task bwa_aln_pe {
     String output_bam = prefix + ".bam"
 
     Float input_fastq_size = (
-        size(read_one_fastq_gz, "GiB") + size(read_two_fastq_gz, "GiB")
+        size(read_one_fastq_gz, "GB") + size(read_two_fastq_gz, "GB")
     )
-    Float reference_size = size(bwa_db_tar_gz, "GiB")
+    Float reference_size = size(bwa_db_tar_gz, "GB")
     Int disk_size_gb = (
         ceil((input_fastq_size + reference_size) * 2) + 5 + modify_disk_size_gb
     )
@@ -242,9 +242,9 @@ task bwa_mem {
 
     String output_bam = prefix + ".bam"
 
-    Float input_fastq_size = size(read_one_fastq_gz, "GiB")
-        + size(read_two_fastq_gz, "GiB")
-    Float reference_size = size(bwa_db_tar_gz, "GiB")
+    Float input_fastq_size = size(read_one_fastq_gz, "GB")
+        + size(read_two_fastq_gz, "GB")
+    Float reference_size = size(bwa_db_tar_gz, "GB")
     Int disk_size_gb = (
         ceil((input_fastq_size + reference_size) * 2) + 10 + modify_disk_size_gb
     )
@@ -324,7 +324,7 @@ task build_bwa_db {
         Int modify_disk_size_gb = 0
     }
 
-    Float input_fasta_size = size(reference_fasta, "GiB")
+    Float input_fasta_size = size(reference_fasta, "GB")
     Int disk_size_gb = ceil(input_fasta_size * 2) + 10 + modify_disk_size_gb
     String bwa_db_out_name = db_name + ".tar.gz"
 

tools/deeptools.wdl

@@ -34,7 +34,7 @@ task bam_coverage {
         Int modify_disk_size_gb = 0
     }
 
-    Float bam_size = size(bam, "GiB")
+    Float bam_size = size(bam, "GB")
     Int disk_size_gb = ceil(bam_size * 1.5) + 10 + modify_disk_size_gb
 
     command <<<

tools/fastqc.wdl

@@ -35,7 +35,7 @@ task fastqc {
 
     String out_tar_gz = prefix + ".tar.gz"
 
-    Float bam_size = size(bam, "GiB")
+    Float bam_size = size(bam, "GB")
     Int disk_size_gb = ceil(bam_size * 2) + 10 + modify_disk_size_gb
 
     command <<<

tools/fq.wdl

@@ -64,8 +64,8 @@ task fqlint {
         Int modify_disk_size_gb = 0
     }
 
-    Float read1_size = size(read_one_fastq, "GiB")
-    Float read2_size = size(read_two_fastq, "GiB")
+    Float read1_size = size(read_one_fastq, "GB")
+    Float read2_size = size(read_two_fastq, "GB")
 
     Int memory_gb = (
         ceil((read1_size + read2_size) * 0.25) + 1 + modify_memory_gb
@@ -133,8 +133,8 @@ task subsample {
         Int modify_disk_size_gb = 0
     }
 
-    Float read1_size = size(read_one_fastq, "GiB")
-    Float read2_size = size(read_two_fastq, "GiB")
+    Float read1_size = size(read_one_fastq, "GB")
+    Float read2_size = size(read_two_fastq, "GB")
 
     Int disk_size_gb = ceil((read1_size + read2_size) * 2) + modify_disk_size_gb
 

tools/gatk4.wdl

@@ -450,7 +450,7 @@ task mark_duplicates_spark {
         Int ncpu = 4
     }
 
-    Float bam_size = size(bam, "GiB")
+    Float bam_size = size(bam, "GB")
     Int memory_gb = min(ceil(bam_size + 15), 50) + modify_memory_gb
     Int disk_size_gb = (
         (