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a-frantza-frantz
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wip: resolving bad merge
1 parent 21a7752 commit a7b661d

6 files changed

Lines changed: 27 additions & 27 deletions

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‎tools/arriba.wdl‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -199,9 +199,9 @@ task arriba {
199199
Int modify_disk_size_gb = 0
200200
}
201201

202-
Int bam_size_gb = ceil(size(bam, "GiB"))
203-
Int disk_size_gb = bam_size_gb + ceil(size(gtf, "GiB")) + ceil(size(reference_fasta_gz,
204-
"GiB")) + modify_disk_size_gb
202+
Int bam_size_gb = ceil(size(bam, "GB"))
203+
Int disk_size_gb = bam_size_gb + ceil(size(gtf, "GB")) + ceil(size(reference_fasta_gz,
204+
"GB")) + modify_disk_size_gb
205205
Int memory_gb = bam_size_gb + modify_memory_gb
206206

207207
command <<<
@@ -301,8 +301,8 @@ task arriba_tsv_to_vcf {
301301
Int modify_disk_size_gb = 0
302302
}
303303

304-
Int input_size_gb = ceil(size(fusions, "GiB"))
305-
Int disk_size_gb = ceil(input_size_gb) + (ceil(size(reference_fasta, "GiB")) * 3) + modify_disk_size_gb
304+
Int input_size_gb = ceil(size(fusions, "GB"))
305+
Int disk_size_gb = ceil(input_size_gb) + (ceil(size(reference_fasta, "GB")) * 3) + modify_disk_size_gb
306306

307307
command <<<
308308
set -euo pipefail
@@ -355,7 +355,7 @@ task arriba_extract_fusion_supporting_alignments {
355355
Int modify_disk_size_gb = 0
356356
}
357357

358-
Int input_size_gb = ceil(size(bam, "GiB"))
358+
Int input_size_gb = ceil(size(bam, "GB"))
359359
Int disk_size_gb = ceil(input_size_gb) + 5 + modify_disk_size_gb
360360

361361
command <<<
@@ -400,7 +400,7 @@ task arriba_annotate_exon_numbers {
400400
Int modify_disk_size_gb = 0
401401
}
402402

403-
Int input_size_gb = ceil(size(gtf, "GiB"))
403+
Int input_size_gb = ceil(size(gtf, "GB"))
404404
Int disk_size_gb = ceil(input_size_gb) + 5 + modify_disk_size_gb
405405

406406
command <<<

‎tools/fq.wdl‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -63,8 +63,8 @@ task fqlint {
6363
Int modify_disk_size_gb = 0
6464
}
6565

66-
Float read1_size = size(read_one_fastq, "GiB")
67-
Float read2_size = size(read_two_fastq, "GiB")
66+
Float read1_size = size(read_one_fastq, "GB")
67+
Float read2_size = size(read_two_fastq, "GB")
6868

6969
Int memory_gb = (ceil((read1_size + read2_size) * 0.25) + 1 + modify_memory_gb)
7070

@@ -131,8 +131,8 @@ task subsample {
131131
Int modify_disk_size_gb = 0
132132
}
133133

134-
Float read1_size = size(read_one_fastq, "GiB")
135-
Float read2_size = size(read_two_fastq, "GiB")
134+
Float read1_size = size(read_one_fastq, "GB")
135+
Float read2_size = size(read_two_fastq, "GB")
136136

137137
Int disk_size_gb = ceil((read1_size + read2_size) * 2) + modify_disk_size_gb
138138

‎tools/gatk4.wdl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -454,7 +454,7 @@ task mark_duplicates_spark {
454454
Int ncpu = 4
455455
}
456456

457-
Float bam_size = size(bam, "GiB")
457+
Float bam_size = size(bam, "GB")
458458
Int memory_gb = min(ceil(bam_size + 15), 50) + modify_memory_gb
459459
Int disk_size_gb = ((if create_bam
460460
then ceil((bam_size * 2) + 10)

‎tools/kraken2.wdl‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -165,7 +165,7 @@ task create_library_from_fastas {
165165

166166
String db_name = "kraken2_custom_library"
167167

168-
Float fastas_size = size(fastas_gz, "GiB")
168+
Float fastas_size = size(fastas_gz, "GB")
169169
Int disk_size_gb = ceil(fastas_size * 5) + 10 + modify_disk_size_gb
170170

171171
command <<<
@@ -260,7 +260,7 @@ task build_db {
260260
Int modify_disk_size_gb = 0
261261
}
262262

263-
Float tarballs_size = size(tarballs, "GiB")
263+
Float tarballs_size = size(tarballs, "GB")
264264
Int disk_size_gb = ceil(tarballs_size * 6) + 10 + modify_disk_size_gb
265265
Int memory_gb = ((if (max_db_size_gb > 0)
266266
then ceil(max_db_size_gb * 1.2)
@@ -383,9 +383,9 @@ task kraken {
383383
Int modify_disk_size_gb = 0
384384
}
385385

386-
Float db_size = size(db, "GiB")
387-
Float read1_size = size(read_one_fastq_gz, "GiB")
388-
Float read2_size = size(read_two_fastq_gz, "GiB")
386+
Float db_size = size(db, "GB")
387+
Float read1_size = size(read_one_fastq_gz, "GB")
388+
Float read2_size = size(read_two_fastq_gz, "GB")
389389
Int disk_size_gb_calculation = (ceil((db_size * 2) + read1_size + read2_size) + 10 + modify_disk_size_gb
390390
)
391391
Int disk_size_gb = (if store_sequences

‎tools/qualimap.wdl‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -48,8 +48,8 @@ task rnaseq {
4848
else ""
4949

5050
Int java_heap_size = ceil(memory_gb * 0.9)
51-
Float bam_size = size(bam, "GiB")
52-
Float gtf_size = size(gtf, "GiB")
51+
Float bam_size = size(bam, "GB")
52+
Float gtf_size = size(gtf, "GB")
5353

5454
# Qualimap has an inefficient name sorting algorithm and will
5555
# use an excessive amount of storage.
@@ -124,7 +124,7 @@ task bamqc {
124124

125125
Int java_heap_size = ceil(memory_gb * 0.9)
126126

127-
Float bam_size = size(bam, "GiB")
127+
Float bam_size = size(bam, "GB")
128128
Int disk_size_gb = ceil(bam_size) + 10 + modify_disk_size_gb
129129

130130
command <<<

‎tools/util.wdl‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -110,7 +110,7 @@ task calc_feature_lengths {
110110
Int modify_disk_size_gb = 0
111111
}
112112

113-
Float gtf_size = size(gtf, "GiB")
113+
Float gtf_size = size(gtf, "GB")
114114
Int disk_size_gb = ceil(gtf_size * 2) + 10 + modify_disk_size_gb
115115

116116
command <<<
@@ -147,7 +147,7 @@ task compression_integrity {
147147
Int modify_disk_size_gb = 0
148148
}
149149

150-
Float file_size = size(bgzipped_file, "GiB")
150+
Float file_size = size(bgzipped_file, "GB")
151151
Int disk_size_gb = ceil(file_size) + 10 + modify_disk_size_gb
152152

153153
command <<<
@@ -186,7 +186,7 @@ task add_to_bam_header {
186186
Int modify_disk_size_gb = 0
187187
}
188188

189-
Float bam_size = size(bam, "GiB")
189+
Float bam_size = size(bam, "GB")
190190
Int disk_size_gb = ceil(bam_size) + 10 + modify_disk_size_gb
191191

192192
String outfile_name = prefix + ".bam"
@@ -228,7 +228,7 @@ task unpack_tarball {
228228
Int modify_disk_size_gb = 0
229229
}
230230

231-
Float tarball_size = size(tarball, "GiB")
231+
Float tarball_size = size(tarball, "GB")
232232
Int disk_size_gb = ceil(tarball_size * 8) + modify_disk_size_gb
233233

234234
command <<<
@@ -286,7 +286,7 @@ task make_coverage_regions_bed {
286286
Int modify_disk_size_gb = 0
287287
}
288288

289-
Float gtf_size = size(gtf, "GiB")
289+
Float gtf_size = size(gtf, "GB")
290290
Int disk_size_gb = ceil(gtf_size * 1.2) + 10 + modify_disk_size_gb
291291

292292
command <<<
@@ -331,7 +331,7 @@ task global_phred_scores {
331331
Int modify_disk_size_gb = 0
332332
}
333333

334-
Float bam_size = size(bam, "GiB")
334+
Float bam_size = size(bam, "GB")
335335
Int disk_size_gb = ceil(bam_size) + 10 + modify_disk_size_gb
336336

337337
String outfile_name = prefix + ".global_PHRED_scores.tsv"
@@ -437,7 +437,7 @@ task split_fastq {
437437
Int ncpu = 2
438438
}
439439

440-
Float fastq_size = size(fastq, "GiB")
440+
Float fastq_size = size(fastq, "GB")
441441
Int disk_size_gb = ceil(fastq_size * 5) + 10 + modify_disk_size_gb
442442

443443
command <<<

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