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dpark01dpark01
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viral-core 2.5.9 to 2.5.10
1 parent baa6141 commit eafb110

11 files changed

Lines changed: 37 additions & 37 deletions

‎pipes/WDL/tasks/tasks_assembly.wdl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -585,7 +585,7 @@ task align_reads {
585585
Boolean skip_mark_dupes = false
586586

587587
Int? machine_mem_gb
588-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
588+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
589589

590590
String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
591591
}
@@ -851,7 +851,7 @@ task run_discordance {
851851
String out_basename = "run"
852852
Int min_coverage = 4
853853

854-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
854+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
855855
}
856856
parameter_meta {
857857
reads_aligned_bam: {

‎pipes/WDL/tasks/tasks_demux.wdl‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ task merge_tarballs {
66
String out_filename
77

88
Int? machine_mem_gb
9-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
9+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
1010
}
1111

1212
Int disk_size = 2625
@@ -181,7 +181,7 @@ task illumina_demux {
181181
# --- options for VM shape ----------------------
182182
Int? machine_mem_gb
183183
Int disk_size = 2625
184-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
184+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
185185
}
186186

187187
parameter_meta {
@@ -860,7 +860,7 @@ task get_illumina_run_metadata {
860860
String? sequencing_center
861861

862862
Int? machine_mem_gb
863-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
863+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
864864
}
865865

866866
parameter_meta {
@@ -984,7 +984,7 @@ task demux_fastqs {
984984
Int? memory_gb
985985
Int? machine_mem_gb
986986
Int disk_size = 750
987-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
987+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
988988
}
989989

990990
parameter_meta {
@@ -1128,7 +1128,7 @@ task merge_demux_metrics {
11281128
input {
11291129
Array[File]+ metrics_files
11301130
String output_filename = "merged_demux_metrics.txt"
1131-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
1131+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
11321132
}
11331133

11341134
parameter_meta {

‎pipes/WDL/tasks/tasks_interhost.wdl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -351,7 +351,7 @@ task index_ref {
351351
File? novocraft_license
352352

353353
Int? machine_mem_gb
354-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
354+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
355355
}
356356

357357
Int disk_size = 100

‎pipes/WDL/tasks/tasks_ncbi.wdl‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -183,7 +183,7 @@ task sequencing_platform_from_bam {
183183
input {
184184
File bam
185185

186-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
186+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
187187
}
188188

189189
command <<<
@@ -293,7 +293,7 @@ task structured_comments {
293293

294294
File? filter_to_ids
295295

296-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
296+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
297297
}
298298
String out_base = basename(assembly_stats_tsv, '.txt')
299299
command <<<
@@ -346,7 +346,7 @@ task structured_comments_from_aligned_bam {
346346
String out_basename = basename(aligned_bam, '.bam')
347347
Boolean is_genome_assembly = true
348348
Boolean sanitize_ids = true
349-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
349+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
350350
}
351351
# see https://www.ncbi.nlm.nih.gov/genbank/structuredcomment/
352352
command <<<
@@ -465,7 +465,7 @@ task rename_fasta_header {
465465

466466
String out_basename = basename(genome_fasta, ".fasta")
467467

468-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
468+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
469469
}
470470
command {
471471
set -e
@@ -630,7 +630,7 @@ task sra_meta_prep {
630630
Boolean paired
631631

632632
String out_name = "sra_metadata.tsv"
633-
String docker="quay.io/broadinstitute/viral-core:2.5.9"
633+
String docker="quay.io/broadinstitute/viral-core:2.5.10"
634634
}
635635
Int disk_size = 100
636636
parameter_meta {

‎pipes/WDL/tasks/tasks_nextstrain.wdl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -332,7 +332,7 @@ task derived_cols {
332332
String? lab_highlight_loc
333333
Array[File] table_map = []
334334

335-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
335+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
336336
Int disk_size = 50
337337
}
338338
parameter_meta {
@@ -900,7 +900,7 @@ task filter_sequences_to_list {
900900

901901
String out_fname = sub(sub(basename(sequences, ".zst"), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
902902
# Prior docker image: "nextstrain/base:build-20240318T173028Z"
903-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
903+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
904904
Int disk_size = 750
905905
}
906906
parameter_meta {

‎pipes/WDL/tasks/tasks_read_utils.wdl‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -84,7 +84,7 @@ task group_bams_by_sample {
8484
task get_bam_samplename {
8585
input {
8686
File bam
87-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
87+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
8888
}
8989
Int disk_size = round(size(bam, "GB")) + 50
9090
command <<<
@@ -111,7 +111,7 @@ task get_sample_meta {
111111
input {
112112
Array[File] samplesheets_extended
113113

114-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
114+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
115115
}
116116
Int disk_size = 50
117117
command <<<
@@ -173,7 +173,7 @@ task merge_and_reheader_bams {
173173
String out_basename = basename(in_bams[0], ".bam")
174174

175175
Boolean run_fastqc = false
176-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
176+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
177177
Int disk_size = 750
178178
Int machine_mem_gb = 4
179179
}
@@ -249,7 +249,7 @@ task rmdup_ubam {
249249
String method = "mvicuna"
250250

251251
Int machine_mem_gb = 7
252-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
252+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
253253
}
254254

255255
Int disk_size = 375 + 2 * ceil(size(reads_unmapped_bam, "GB"))
@@ -308,7 +308,7 @@ task downsample_bams {
308308
Boolean deduplicateAfter = false
309309

310310
Int? machine_mem_gb
311-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
311+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
312312
}
313313

314314
Int disk_size = 750
@@ -375,7 +375,7 @@ task FastqToUBAM {
375375
Int cpus = 2
376376
Int mem_gb = 4
377377
Int disk_size = 750
378-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
378+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
379379
}
380380
parameter_meta {
381381
fastq_1: { description: "Unaligned read1 file in fastq format", patterns: ["*.fastq", "*.fastq.gz", "*.fq", "*.fq.gz"] }
@@ -429,7 +429,7 @@ task read_depths {
429429
File aligned_bam
430430

431431
String out_basename = basename(aligned_bam, '.bam')
432-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
432+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
433433
}
434434
Int disk_size = 200
435435
command <<<

‎pipes/WDL/tasks/tasks_reports.wdl‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@ task alignment_metrics {
1515
Int max_amplicons=500
1616

1717
Int machine_mem_gb=16
18-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
18+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
1919
}
2020

2121
String out_basename = basename(aligned_bam, ".bam")
@@ -143,7 +143,7 @@ task plot_coverage {
143143
String? plotXLimits # of the form "min max" (ints, space between)
144144
String? plotYLimits # of the form "min max" (ints, space between)
145145
146-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
146+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
147147
}
148148

149149
Int disk_size = 375
@@ -290,7 +290,7 @@ task coverage_report {
290290
Array[File] mapped_bam_idx = [] # optional.. speeds it up if you provide it, otherwise we auto-index
291291
String out_report_name = "coverage_report.txt"
292292

293-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
293+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
294294
}
295295

296296
Int disk_size = 375
@@ -365,7 +365,7 @@ task fastqc {
365365
input {
366366
File reads_bam
367367

368-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
368+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
369369
}
370370
parameter_meta {
371371
reads_bam:{
@@ -413,7 +413,7 @@ task align_and_count {
413413
Boolean keep_duplicates_when_filtering = false
414414

415415
Int? machine_mem_gb
416-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
416+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
417417
}
418418

419419
String reads_basename=basename(reads_bam, ".bam")
@@ -536,7 +536,7 @@ task align_and_count_summary {
536536
537537
String output_prefix = "count_summary"
538538
539-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
539+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
540540
}
541541
542542
Int disk_size = 100

‎pipes/WDL/tasks/tasks_taxon_filter.wdl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -211,7 +211,7 @@ task merge_one_per_sample {
211211
Boolean rmdup = false
212212

213213
Int machine_mem_gb = 7
214-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
214+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
215215
}
216216

217217
Int disk_size = 750

‎pipes/WDL/tasks/tasks_terra.wdl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@ task gcs_copy {
3333

3434
task check_terra_env {
3535
input {
36-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
36+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
3737
}
3838
meta {
3939
description: "task for inspection of backend to determine whether the task is running on Terra and/or GCP"
@@ -440,7 +440,7 @@ task create_or_update_sample_tables {
440440
String sample_table_name = "sample"
441441
String library_table_name = "library"
442442

443-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
443+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
444444
}
445445

446446
meta {

‎pipes/WDL/tasks/tasks_utils.wdl‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -52,7 +52,7 @@ task unpack_archive_to_bucket_path {
5252
# execution and resource requirements
5353
Int disk_size = 500
5454
Int machine_mem_gb = 128
55-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
55+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
5656
}
5757

5858
parameter_meta {
@@ -293,7 +293,7 @@ task zcat {
293293
{ if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
294294
>>>
295295
runtime {
296-
docker: "quay.io/broadinstitute/viral-core:2.5.9"
296+
docker: "quay.io/broadinstitute/viral-core:2.5.10"
297297
memory: "1 GB"
298298
cpu: cpus
299299
disks: "local-disk " + disk_size + " LOCAL"
@@ -857,7 +857,7 @@ task tsv_join {
857857
runtime {
858858
memory: "~{machine_mem_gb} GB"
859859
cpu: 4
860-
docker: "quay.io/broadinstitute/viral-core:2.5.9"
860+
docker: "quay.io/broadinstitute/viral-core:2.5.10"
861861
disks: "local-disk " + disk_size + " HDD"
862862
disk: disk_size + " GB" # TES
863863
dx_instance_type: "mem1_ssd1_v2_x4"
@@ -944,7 +944,7 @@ task tsv_stack {
944944
input {
945945
Array[File]+ input_tsvs
946946
String out_basename
947-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
947+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
948948
}
949949

950950
Int disk_size = 50
@@ -1215,7 +1215,7 @@ task filter_sequences_by_length {
12151215
File sequences_fasta
12161216
Int min_non_N = 1
12171217

1218-
String docker = "quay.io/broadinstitute/viral-core:2.5.9"
1218+
String docker = "quay.io/broadinstitute/viral-core:2.5.10"
12191219
Int disk_size = 750
12201220
}
12211221
parameter_meta {

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