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chore: bump viral-ngs to 3.0.11 across all remaining task files
Updates tasks_terra, tasks_utils, tasks_taxon_filter, tasks_nextstrain, tasks_megablast, tasks_ncbi, tasks_assembly, tasks_demux, tasks_interhost, tasks_intrahost to match requirements-modules.txt. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
1 parent 4dc7ec3 commit c3e7209

10 files changed

Lines changed: 60 additions & 60 deletions

‎pipes/WDL/tasks/tasks_assembly.wdl‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ task assemble {
1616

1717
Int? machine_mem_gb
1818
Int? cpu
19-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
19+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-assemble"
2020
}
2121
parameter_meta{
2222
reads_unmapped_bam: {
@@ -124,7 +124,7 @@ task select_references {
124124
Int? skani_c
125125
Int? skani_n
126126

127-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
127+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-assemble"
128128
Int machine_mem_gb = 4
129129
Int cpu = 2
130130
Int disk_size = 100
@@ -223,7 +223,7 @@ task scaffold {
223223
Float? scaffold_min_pct_contig_aligned
224224

225225
Int? machine_mem_gb
226-
String docker="quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
226+
String docker="quay.io/broadinstitute/viral-ngs:3.0.11-assemble"
227227

228228
# do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
229229
String sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades")
@@ -475,7 +475,7 @@ task skani_triangle {
475475
Int compression_factor = 10
476476
Int min_aligned_frac = 15
477477

478-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
478+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-assemble"
479479
Int machine_mem_gb = 8
480480
Int cpu = 4
481481
Int disk_size = 100
@@ -715,7 +715,7 @@ task align_reads {
715715
716716
Int? cpu
717717
Int? machine_mem_gb
718-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
718+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
719719

720720
String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
721721
}
@@ -878,7 +878,7 @@ task refine_assembly_with_aligned_reads {
878878
Int min_coverage = 3
879879

880880
Int machine_mem_gb = 8
881-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
881+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-assemble"
882882
}
883883

884884
Int disk_size = 375
@@ -1014,7 +1014,7 @@ task run_discordance {
10141014
String out_basename = "run"
10151015
Int min_coverage = 4
10161016

1017-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
1017+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
10181018
}
10191019
parameter_meta {
10201020
reads_aligned_bam: {
@@ -1260,7 +1260,7 @@ task wgsim {
12601260
Int? random_seed
12611261

12621262
Int machine_mem_gb = 7
1263-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-assemble"
1263+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-assemble"
12641264
}
12651265

12661266
parameter_meta {

‎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-ngs:3.0.10-core"
9+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
1010
}
1111

1212
Int disk_size = 2625
@@ -179,7 +179,7 @@ task illumina_demux {
179179
Int? machine_mem_gb
180180
# Note: GCP local SSDs must be allocated in pairs (2, 4, 8, 16, 24 × 375GB), so use 3000 (8 SSDs) instead of 2625 (7 SSDs)
181181
Int disk_size = 3000
182-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
182+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
183183
}
184184

185185
parameter_meta {
@@ -817,7 +817,7 @@ task get_illumina_run_metadata {
817817
String? sequencing_center
818818

819819
Int? machine_mem_gb
820-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
820+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
821821
}
822822

823823
parameter_meta {
@@ -920,7 +920,7 @@ task demux_fastqs {
920920
Int? machine_mem_gb
921921
Int max_cpu = 32 # Maximum CPU cap for autoscaling (use 16 for 2-barcode, 64 for 3-barcode)
922922
Int disk_size = 750
923-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
923+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
924924
}
925925

926926
# Calculate total input size for autoscaling
@@ -1048,7 +1048,7 @@ task merge_demux_metrics {
10481048
input {
10491049
Array[File]+ metrics_files
10501050
String output_filename = "merged_demux_metrics.txt"
1051-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
1051+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
10521052
}
10531053

10541054
parameter_meta {

‎pipes/WDL/tasks/tasks_interhost.wdl‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -160,7 +160,7 @@ task multi_align_mafft_ref {
160160
Float? mafft_gapOpeningPenalty
161161

162162
Int? machine_mem_gb
163-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
163+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
164164
}
165165

166166
String fasta_basename = basename(reference_fasta, '.fasta')
@@ -206,7 +206,7 @@ task multi_align_mafft {
206206
Float? mafft_gapOpeningPenalty
207207

208208
Int? machine_mem_gb
209-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
209+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
210210
}
211211

212212
Int disk_size = 200
@@ -348,7 +348,7 @@ task index_ref {
348348
File? novocraft_license
349349

350350
Int? machine_mem_gb
351-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
351+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
352352
}
353353

354354
Int disk_size = 100
@@ -470,7 +470,7 @@ task merge_vcfs_gatk {
470470
File ref_fasta
471471

472472
Int? machine_mem_gb
473-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
473+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
474474

475475
String output_prefix = "merged"
476476
}

‎pipes/WDL/tasks/tasks_intrahost.wdl‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -138,7 +138,7 @@ task lofreq {
138138
Int cpu = 4
139139

140140
String out_basename = basename(aligned_bam, '.bam')
141-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
141+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
142142
}
143143
Int disk_size = ceil(5 * size(aligned_bam, "GB") + 50)
144144
command <<<
@@ -215,7 +215,7 @@ task isnvs_per_sample {
215215
Boolean removeDoublyMappedReads = true
216216

217217
Int? machine_mem_gb
218-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
218+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
219219

220220
String sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped")
221221
}
@@ -257,7 +257,7 @@ task isnvs_vcf {
257257
Boolean naiveFilter = false
258258

259259
Int? machine_mem_gb
260-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
260+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
261261
}
262262

263263
parameter_meta {
@@ -330,7 +330,7 @@ task annotate_vcf_snpeff {
330330
String? emailAddress
331331

332332
Int? machine_mem_gb
333-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
333+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
334334

335335
String output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
336336
}

‎pipes/WDL/tasks/tasks_megablast.wdl‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@ task trim_rmdup_subsamp {
1515
Int cpu = 16
1616
Int disk_size_gb = 100
1717

18-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
18+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
1919
}
2020

2121
parameter_meta {
@@ -75,7 +75,7 @@ task lca_megablast {
7575
Int cpu = 16
7676
Int disk_size_gb = 300
7777

78-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-classify"
78+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-classify"
7979
}
8080
parameter_meta {
8181
trimmed_fasta: {

‎pipes/WDL/tasks/tasks_ncbi.wdl‎

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ task download_fasta {
66
Array[String]+ accessions
77
String emailAddress
88

9-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
9+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
1010
}
1111

1212
command <<<
@@ -41,7 +41,7 @@ task download_fasta_from_accession_string {
4141
String out_prefix
4242
String emailAddress
4343

44-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
44+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
4545
}
4646

4747
command <<<
@@ -92,7 +92,7 @@ task download_annotations {
9292
String emailAddress
9393
String combined_out_prefix
9494

95-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
95+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
9696
}
9797

9898
command <<<
@@ -133,7 +133,7 @@ task download_ref_genomes_from_tsv {
133133
File ref_genomes_tsv # [tax_id, isolate_prefix, taxname, colon_delim_accession_list]
134134
String emailAddress
135135

136-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
136+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
137137
}
138138

139139
command <<<
@@ -179,7 +179,7 @@ task sequencing_platform_from_bam {
179179
input {
180180
File bam
181181

182-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
182+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
183183
}
184184

185185
command <<<
@@ -233,7 +233,7 @@ task align_and_annot_transfer_single {
233233

234234
String out_basename = basename(genome_fasta, '.fasta')
235235
Int machine_mem_gb = 30
236-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
236+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
237237
}
238238

239239
parameter_meta {
@@ -287,7 +287,7 @@ task structured_comments {
287287

288288
File? filter_to_ids
289289

290-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
290+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
291291
}
292292
String out_base = basename(assembly_stats_tsv, '.txt')
293293
command <<<
@@ -339,7 +339,7 @@ task structured_comments_from_aligned_bam {
339339
String out_basename = basename(aligned_bam, '.bam')
340340
Boolean is_genome_assembly = true
341341
Boolean sanitize_ids = true
342-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
342+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
343343
}
344344
# see https://www.ncbi.nlm.nih.gov/genbank/structuredcomment/
345345
command <<<
@@ -456,7 +456,7 @@ task rename_fasta_header {
456456

457457
String out_basename = basename(genome_fasta, ".fasta")
458458

459-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
459+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
460460
}
461461
command <<<
462462
set -e
@@ -618,7 +618,7 @@ task sra_meta_prep {
618618
Boolean paired
619619

620620
String out_name = "sra_metadata.tsv"
621-
String docker="quay.io/broadinstitute/viral-ngs:3.0.10-core"
621+
String docker="quay.io/broadinstitute/viral-ngs:3.0.11-core"
622622
}
623623
Int disk_size = 100
624624
parameter_meta {
@@ -1230,7 +1230,7 @@ task table2asn {
12301230

12311231
String out_basename = basename(assembly_fasta, ".fasta")
12321232
Int machine_mem_gb = 8
1233-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo" # this could be a simpler docker image, we don't use anything beyond table2asn itself
1233+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo" # this could be a simpler docker image, we don't use anything beyond table2asn itself
12341234
}
12351235
Int disk_size = 50
12361236

@@ -1321,7 +1321,7 @@ task package_special_genbank_ftp_submission {
13211321
String account_name
13221322
String wizard="BankIt_SARSCoV2_api"
13231323

1324-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-baseimage"
1324+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-baseimage"
13251325
}
13261326
command <<<
13271327
set -e
@@ -1385,7 +1385,7 @@ task genbank_special_taxa {
13851385
Int taxid
13861386
File taxdump_tgz
13871387
File vadr_by_taxid_tsv # "gs://pathogen-public-dbs/viral-references/annotation/vadr/vadr-by-taxid.tsv"
1388-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-classify"
1388+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-classify"
13891389
}
13901390

13911391
command <<<

‎pipes/WDL/tasks/tasks_nextstrain.wdl‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ task taxid_to_nextclade_dataset_name {
55
Int taxid
66
File taxdump_tgz
77
File nextclade_by_taxid_tsv # "gs://pathogen-public-dbs/viral-references/typing/nextclade-by-taxid.tsv"
8-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-classify"
8+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-classify"
99
}
1010
command <<<
1111
set -e
@@ -328,7 +328,7 @@ task derived_cols {
328328
String? lab_highlight_loc
329329
Array[File] table_map = []
330330

331-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
331+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
332332
Int disk_size = 50
333333
}
334334
parameter_meta {
@@ -889,7 +889,7 @@ task filter_sequences_to_list {
889889

890890
String out_fname = sub(sub(basename(sequences, ".zst"), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
891891
# Prior docker image: "nextstrain/base:build-20240318T173028Z"
892-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-core"
892+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-core"
893893
Int disk_size = 750
894894
}
895895
parameter_meta {
@@ -989,7 +989,7 @@ task mafft_one_chr {
989989
Boolean large = false
990990
Boolean memsavetree = false
991991

992-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
992+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
993993
Int mem_size = 500
994994
Int cpus = 64
995995
Int disk_size = 750
@@ -1078,7 +1078,7 @@ task mafft_one_chr_chunked {
10781078
Int batch_chunk_size = 2000
10791079
Int threads_per_job = 2
10801080

1081-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.10-phylo"
1081+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.11-phylo"
10821082
Int mem_size = 32
10831083
Int cpus = 64
10841084
Int disk_size = 750

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