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dpark01dpark01
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bump a bunch of docker versions
1 parent 54c2cc7 commit aa1a086

16 files changed

Lines changed: 106 additions & 106 deletions

‎pipes/WDL/tasks/tasks_assembly.wdl‎

Lines changed: 9 additions & 9 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:3.0.15-assemble"
19+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-assemble"
127+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-assemble"
226+
String docker="quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-assemble"
478+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-assemble"
479479
Int machine_mem_gb = 8
480480
Int cpu = 4
481481
Int disk_size = 100
@@ -636,7 +636,7 @@ task ivar_trim_stats {
636636
String out_basename = "ivar_trim_stats"
637637
String flowcell = ""
638638

639-
String docker = "quay.io/broadinstitute/py3-bio:0.1.8"
639+
String docker = "quay.io/broadinstitute/py3-bio:0.1.9"
640640
}
641641
parameter_meta {
642642
ivar_trim_stats_tsv: {
@@ -715,7 +715,7 @@ task align_reads {
715715
716716
Int? cpu
717717
Int? machine_mem_gb
718-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-core"
718+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-core"
719719

720720
String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
721721
}
@@ -879,7 +879,7 @@ task refine_assembly_with_aligned_reads {
879879
Int? max_coverage = 4000
880880

881881
Int machine_mem_gb = 8
882-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-assemble"
882+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-assemble"
883883
}
884884

885885
Int disk_size = 375
@@ -1021,7 +1021,7 @@ task run_discordance {
10211021
Int min_coverage = 4
10221022

10231023
Int machine_mem_gb = 4
1024-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-core"
1024+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-core"
10251025
}
10261026
parameter_meta {
10271027
reads_aligned_bam: {
@@ -1267,7 +1267,7 @@ task wgsim {
12671267
Int? random_seed
12681268

12691269
Int machine_mem_gb = 7
1270-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-assemble"
1270+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-assemble"
12711271
}
12721272

12731273
parameter_meta {

‎pipes/WDL/tasks/tasks_demux.wdl‎

Lines changed: 6 additions & 6 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:3.0.15-core"
9+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-core"
1010
}
1111

1212
Int disk_size = 2625
@@ -97,7 +97,7 @@ task revcomp_i5 {
9797
input {
9898
File old_sheet
9999
Boolean revcomp=true
100-
String docker = "quay.io/broadinstitute/py3-bio:0.1.8"
100+
String docker = "quay.io/broadinstitute/py3-bio:0.1.9"
101101
}
102102
String new_base = basename(basename(old_sheet, '.txt'), '.tsv')
103103
Int disk_size = 50
@@ -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:3.0.15-core"
182+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-core"
820+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-core"
923+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-core"
1051+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-phylo"
163+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-phylo"
209+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-core"
351+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-phylo"
473+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-phylo"
141+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-phylo"
218+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-phylo"
260+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-phylo"
333+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-core"
18+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-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:3.0.15-classify"
78+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
7979
}
8080
parameter_meta {
8181
trimmed_fasta: {

‎pipes/WDL/tasks/tasks_metagenomics.wdl‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -216,7 +216,7 @@ task kraken2 {
216216
Int? min_base_qual
217217

218218
Int machine_mem_gb = 90
219-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-classify"
219+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
220220
}
221221

222222
parameter_meta {
@@ -348,7 +348,7 @@ task report_primary_kraken_taxa {
348348
File kraken_summary_report
349349
String focal_taxon = "Viruses"
350350

351-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-classify"
351+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
352352
}
353353
String out_basename = basename(kraken_summary_report, '.txt')
354354
Int disk_size = 50
@@ -397,7 +397,7 @@ task filter_refs_to_found_taxa {
397397
File taxdump_tgz
398398
Int min_read_count = 100
399399

400-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-classify"
400+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
401401
}
402402
String ref_basename = basename(taxid_to_ref_accessions_tsv, '.tsv')
403403
String hits_basename = basename(focal_report_tsv, '.tsv')
@@ -447,7 +447,7 @@ task build_kraken2_db {
447447
Int? zstd_compression_level
448448

449449
Int machine_mem_gb = 100
450-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-classify"
450+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
451451
}
452452

453453
Int disk_size = 750
@@ -588,7 +588,7 @@ task blastx {
588588
File krona_taxonomy_db_tgz
589589

590590
Int machine_mem_gb = 8
591-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-classify"
591+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
592592
}
593593

594594
parameter_meta {
@@ -677,7 +677,7 @@ task krona {
677677
Int? magnitude_column
678678

679679
Int machine_mem_gb = 3
680-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-classify"
680+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
681681
}
682682

683683
Int disk_size = 50
@@ -782,7 +782,7 @@ task filter_bam_to_taxa {
782782
String out_filename_suffix = "filtered"
783783

784784
Int machine_mem_gb = 8
785-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-classify"
785+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
786786
}
787787

788788
String out_basename = basename(classified_bam, ".bam") + "." + out_filename_suffix
@@ -874,7 +874,7 @@ task kaiju {
874874
File krona_taxonomy_db_tgz # taxonomy/taxonomy.tab
875875
876876
Int machine_mem_gb = 100
877-
String docker = "quay.io/broadinstitute/viral-ngs:3.0.15-classify"
877+
String docker = "quay.io/broadinstitute/viral-ngs:3.0.16-classify"
878878
}
879879

880880
String input_basename = basename(reads_unmapped_bam, ".bam")

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