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Merged
adthrasher merged 2 commits into from
Feb 23, 2026
Merged

chore: GiB -> GB #302

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63f0915
chore: GiB -> GB
adthrasher Feb 23, 2026
7a2a500
chore: update CHANGELOGs
adthrasher Feb 23, 2026
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6 changes: 6 additions & 0 deletions data_structures/CHANGELOG.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion data_structures/read_group.wdl
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Expand Up @@ -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 <<<
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2 changes: 1 addition & 1 deletion template/task-examples.wdl
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Expand Up @@ -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
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1 change: 1 addition & 0 deletions tools/CHANGELOG.md
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Expand Up @@ -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

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14 changes: 7 additions & 7 deletions tools/arriba.wdl
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Expand Up @@ -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

Expand Down Expand Up @@ -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 <<<
Expand Down Expand Up @@ -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 <<<
Expand Down Expand Up @@ -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 <<<
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16 changes: 8 additions & 8 deletions tools/bwa.wdl
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Expand Up @@ -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
)
Expand Down Expand Up @@ -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
)
Expand Down Expand Up @@ -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
)
Expand Down Expand Up @@ -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"

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2 changes: 1 addition & 1 deletion tools/deeptools.wdl
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Expand Up @@ -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 <<<
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2 changes: 1 addition & 1 deletion tools/fastqc.wdl
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Expand Up @@ -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 <<<
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8 changes: 4 additions & 4 deletions tools/fq.wdl
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Expand Up @@ -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
Expand Down Expand Up @@ -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

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2 changes: 1 addition & 1 deletion tools/gatk4.wdl
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Expand Up @@ -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 = (
(
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4 changes: 2 additions & 2 deletions tools/htseq.wdl
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Expand Up @@ -93,8 +93,8 @@ task count {

String outfile_name = prefix + ".feature-counts.txt"

Float bam_size = size(bam, "GiB")
Float gtf_size = size(gtf, "GiB")
Float bam_size = size(bam, "GB")
Float gtf_size = size(gtf, "GB")

Int memory_gb = (if pos_sorted then ceil(bam_size) + 4 else 4) + modify_memory_gb

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10 changes: 5 additions & 5 deletions tools/kraken2.wdl
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Expand Up @@ -161,7 +161,7 @@ task create_library_from_fastas {

String db_name = "kraken2_custom_library"

Float fastas_size = size(fastas_gz, "GiB")
Float fastas_size = size(fastas_gz, "GB")
Int disk_size_gb = ceil(fastas_size * 5) + 10 + modify_disk_size_gb

command <<<
Expand Down Expand Up @@ -247,7 +247,7 @@ task build_db {
Int modify_disk_size_gb = 0
}

Float tarballs_size = size(tarballs, "GiB")
Float tarballs_size = size(tarballs, "GB")
Int disk_size_gb = ceil(tarballs_size * 6) + 10 + modify_disk_size_gb
Int memory_gb = (
(
Expand Down Expand Up @@ -373,9 +373,9 @@ task kraken {
Int modify_disk_size_gb = 0
}

Float db_size = size(db, "GiB")
Float read1_size = size(read_one_fastq_gz, "GiB")
Float read2_size = size(read_two_fastq_gz, "GiB")
Float db_size = size(db, "GB")
Float read1_size = size(read_one_fastq_gz, "GB")
Float read2_size = size(read_two_fastq_gz, "GB")
Int disk_size_gb_calculation = (
ceil((db_size * 2) + read1_size + read2_size) + 10 + modify_disk_size_gb
)
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2 changes: 1 addition & 1 deletion tools/librarian.wdl
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Expand Up @@ -32,7 +32,7 @@ task librarian {
Int modify_disk_size_gb = 0
}

Float read1_size = size(read_one_fastq, "GiB")
Float read1_size = size(read_one_fastq, "GB")
Int disk_size_gb = (
ceil(read1_size) + 10 + modify_disk_size_gb
)
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2 changes: 1 addition & 1 deletion tools/md5sum.wdl
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Expand Up @@ -20,7 +20,7 @@ task compute_checksum {
Int modify_disk_size_gb = 0
}

Float file_size = size(file, "GiB")
Float file_size = size(file, "GB")
Int disk_size_gb = ceil(file_size) + 10 + modify_disk_size_gb

String outfile_name = basename(file) + ".md5"
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2 changes: 1 addition & 1 deletion tools/mosdepth.wdl
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Expand Up @@ -38,7 +38,7 @@ task 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) + 10 + modify_disk_size_gb

command <<<
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2 changes: 1 addition & 1 deletion tools/multiqc.wdl
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Expand Up @@ -28,7 +28,7 @@ task multiqc {
Int modify_disk_size_gb = 0
}

Float input_size = size(files, "GiB")
Float input_size = size(files, "GB")
Int disk_size_gb = ceil(input_size) * 2 + modify_disk_size_gb

command <<<
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12 changes: 6 additions & 6 deletions tools/ngsderive.wdl
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Expand Up @@ -47,7 +47,7 @@ task strandedness {
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 <<<
Expand Down Expand Up @@ -117,7 +117,7 @@ task instrument {
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 <<<
Expand Down Expand Up @@ -176,7 +176,7 @@ task read_length {
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 <<<
Expand Down Expand Up @@ -233,7 +233,7 @@ task encoding {
Int modify_disk_size_gb = 0
}

Float files_size = size(ngs_files, "GiB")
Float files_size = size(ngs_files, "GB")
Int disk_size_gb = ceil(files_size) + 10 + modify_disk_size_gb

command <<<
Expand Down Expand Up @@ -301,7 +301,7 @@ task junction_annotation {
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 <<<
Expand Down Expand Up @@ -397,7 +397,7 @@ task endedness {
Int modify_disk_size_gb = 0
}

Float bam_size = size(bam, "GiB")
Float bam_size = size(bam, "GB")
Int memory_gb = (
if calc_rpt
then (
Expand Down
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