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tomkinsctomkinsc
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bump viral docker images to ones based on viral-core 2.1.12 (#180)
1 parent 7b6dd91 commit 87066a4

13 files changed

+57
-54
lines changed

‎pipes/WDL/tasks/tasks_assembly.wdl

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@ task assemble {
1515
String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt")
1616

1717
Int? machine_mem_gb
18-
String docker="quay.io/broadinstitute/viral-assemble:2.1.10.0"
18+
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
1919
}
2020

2121
command {
@@ -80,7 +80,7 @@ task scaffold {
8080
Float? scaffold_min_pct_contig_aligned
8181

8282
Int? machine_mem_gb
83-
String docker="quay.io/broadinstitute/viral-assemble:2.1.10.0"
83+
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
8484

8585
# do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
8686
String sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades")
@@ -226,7 +226,7 @@ task align_reads {
226226
Boolean? skip_mark_dupes=false
227227

228228
Int? machine_mem_gb
229-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
229+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
230230

231231
String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
232232
}
@@ -342,7 +342,7 @@ task refine_assembly_with_aligned_reads {
342342
Int? min_coverage=3
343343

344344
Int? machine_mem_gb
345-
String docker="quay.io/broadinstitute/viral-assemble:2.1.10.0"
345+
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
346346
}
347347

348348
parameter_meta {
@@ -434,7 +434,7 @@ task refine {
434434
Int? min_coverage=1
435435

436436
Int? machine_mem_gb
437-
String docker="quay.io/broadinstitute/viral-assemble:2.1.10.0"
437+
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
438438

439439
String assembly_basename=basename(basename(assembly_fasta, ".fasta"), ".scaffold")
440440
}
@@ -504,7 +504,7 @@ task refine_2x_and_plot {
504504
String? plot_coverage_novoalign_options="-r Random -l 40 -g 40 -x 20 -t 100 -k"
505505

506506
Int? machine_mem_gb
507-
String docker="quay.io/broadinstitute/viral-assemble:2.1.10.0"
507+
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
508508

509509
# do this in two steps in case the input doesn't actually have "cleaned" in the name
510510
String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned")
@@ -636,7 +636,7 @@ task run_discordance {
636636
String out_basename = "run"
637637
Int min_coverage=4
638638

639-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
639+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
640640
}
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642642
command {

‎pipes/WDL/tasks/tasks_demux.wdl

Lines changed: 2 additions & 2 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:2.1.10"
9+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
1010
}
1111

1212
command {
@@ -60,7 +60,7 @@ task illumina_demux {
6060
Boolean? forceGC=true
6161

6262
Int? machine_mem_gb
63-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
63+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
6464
}
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6666
command {

‎pipes/WDL/tasks/tasks_interhost.wdl

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ task multi_align_mafft_ref {
99
Float? mafft_gapOpeningPenalty
1010

1111
Int? machine_mem_gb
12-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
12+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
1313
}
1414

1515
String fasta_basename = basename(reference_fasta, '.fasta')
@@ -53,7 +53,7 @@ task multi_align_mafft {
5353
Float? mafft_gapOpeningPenalty
5454

5555
Int? machine_mem_gb
56-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
56+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
5757
}
5858

5959
command {
@@ -142,7 +142,7 @@ task index_ref {
142142
File? novocraft_license
143143

144144
Int? machine_mem_gb
145-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
145+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
146146
}
147147

148148
command {
@@ -252,7 +252,7 @@ task merge_vcfs_gatk {
252252
File ref_fasta
253253

254254
Int? machine_mem_gb
255-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
255+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
256256

257257
String output_prefix = "merged"
258258
}

‎pipes/WDL/tasks/tasks_intrahost.wdl

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ task isnvs_per_sample {
1111
Boolean removeDoublyMappedReads=true
1212

1313
Int? machine_mem_gb
14-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
14+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
1515

1616
String sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped")
1717
}
@@ -52,7 +52,7 @@ task isnvs_vcf {
5252
Boolean naiveFilter=false
5353

5454
Int? machine_mem_gb
55-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
55+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
5656
}
5757

5858
parameter_meta {
@@ -125,7 +125,7 @@ task annotate_vcf_snpeff {
125125
String? emailAddress
126126

127127
Int? machine_mem_gb
128-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
128+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
129129

130130
String output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
131131
}

‎pipes/WDL/tasks/tasks_metagenomics.wdl

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ task krakenuniq {
1111
File krona_taxonomy_db_tgz # taxonomy.tab
1212
1313
Int? machine_mem_gb
14-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
14+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
1515
}
1616

1717
parameter_meta {
@@ -136,7 +136,7 @@ task build_krakenuniq_db {
136136
Int? zstd_compression_level
137137

138138
Int? machine_mem_gb
139-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
139+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
140140
}
141141

142142
command {
@@ -202,7 +202,7 @@ task kraken2 {
202202
Int? min_base_qual
203203

204204
Int? machine_mem_gb
205-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
205+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
206206
}
207207

208208
parameter_meta {
@@ -334,7 +334,7 @@ task build_kraken2_db {
334334
Int? zstd_compression_level
335335

336336
Int? machine_mem_gb
337-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
337+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
338338
}
339339

340340
parameter_meta {
@@ -472,7 +472,7 @@ task blastx {
472472
File krona_taxonomy_db_tgz
473473

474474
Int? machine_mem_gb
475-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
475+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
476476
}
477477

478478
parameter_meta {
@@ -559,7 +559,7 @@ task krona {
559559
Int? magnitude_column
560560

561561
Int? machine_mem_gb
562-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
562+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
563563
}
564564

565565
command {
@@ -658,7 +658,7 @@ task filter_bam_to_taxa {
658658
String out_filename_suffix = "filtered"
659659

660660
Int? machine_mem_gb
661-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
661+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
662662
}
663663

664664
String out_basename = basename(classified_bam, ".bam") + "." + out_filename_suffix
@@ -743,7 +743,7 @@ task kaiju {
743743
File krona_taxonomy_db_tgz # taxonomy/taxonomy.tab
744744
745745
Int? machine_mem_gb
746-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
746+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
747747
}
748748

749749
String input_basename = basename(reads_unmapped_bam, ".bam")

‎pipes/WDL/tasks/tasks_ncbi.wdl

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -25,7 +25,7 @@ task download_fasta {
2525
Array[String]+ accessions
2626
String emailAddress
2727

28-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
28+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
2929
}
3030

3131
command {
@@ -56,7 +56,7 @@ task download_annotations {
5656
String emailAddress
5757
String combined_out_prefix
5858

59-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
59+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
6060
}
6161

6262
command {
@@ -100,7 +100,7 @@ task annot_transfer {
100100
File reference_fasta
101101
Array[File]+ reference_feature_table
102102

103-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
103+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
104104
}
105105

106106
parameter_meta {
@@ -153,7 +153,7 @@ task align_and_annot_transfer_single {
153153
Array[File]+ reference_fastas
154154
Array[File]+ reference_feature_tables
155155

156-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
156+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
157157
}
158158

159159
parameter_meta {
@@ -208,7 +208,7 @@ task biosample_to_genbank {
208208
Int num_segments=1
209209
Int taxid
210210

211-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
211+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
212212
}
213213
String base = basename(biosample_attributes, ".txt")
214214
command {
@@ -254,7 +254,7 @@ task prepare_genbank {
254254
String? assembly_method_version
255255

256256
Int? machine_mem_gb
257-
String docker="quay.io/broadinstitute/viral-phylo:2.1.10.0"
257+
String docker="quay.io/broadinstitute/viral-phylo:2.1.12.0"
258258
}
259259

260260
parameter_meta {

‎pipes/WDL/tasks/tasks_nextstrain.wdl

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -263,7 +263,7 @@ task mafft_one_chr {
263263
Boolean large = false
264264
Boolean memsavetree = false
265265
266-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.10.0"
266+
String docker = "quay.io/broadinstitute/viral-phylo:2.1.12.0"
267267
Int mem_size = 60
268268
Int cpus = 32
269269
}

‎pipes/WDL/tasks/tasks_read_utils.wdl

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ task merge_and_reheader_bams {
1111
File? reheader_table
1212
String out_basename
1313

14-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
14+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
1515
}
1616

1717
command {
@@ -71,7 +71,7 @@ task rmdup_ubam {
7171
String method="mvicuna"
7272

7373
Int? machine_mem_gb
74-
String? docker="quay.io/broadinstitute/viral-core:2.1.10"
74+
String? docker="quay.io/broadinstitute/viral-core:2.1.12"
7575
}
7676

7777
parameter_meta {
@@ -125,7 +125,7 @@ task downsample_bams {
125125
Boolean? deduplicateAfter=false
126126

127127
Int? machine_mem_gb
128-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
128+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
129129
}
130130

131131
command {
@@ -184,7 +184,7 @@ task FastqToUBAM {
184184
String? platform_name
185185
String? sequencing_center
186186

187-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
187+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
188188
}
189189
parameter_meta {
190190
fastq_1: { description: "Unaligned read1 file in fastq format", patterns: ["*.fastq", "*.fastq.gz", "*.fq", "*.fq.gz"] }

‎pipes/WDL/tasks/tasks_reports.wdl

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ task plot_coverage {
1010
Boolean bin_large_plots=false
1111
String? binning_summary_statistic="max" # max or min
1212
13-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
13+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
1414
}
1515

1616
command {
@@ -85,7 +85,7 @@ task coverage_report {
8585
Array[File] mapped_bam_idx # optional.. speeds it up if you provide it, otherwise we auto-index
8686
String out_report_name="coverage_report.txt"
8787

88-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
88+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
8989
}
9090

9191
command {
@@ -115,7 +115,7 @@ task fastqc {
115115
input {
116116
File reads_bam
117117

118-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
118+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
119119
}
120120

121121
String reads_basename=basename(reads_bam, ".bam")
@@ -148,7 +148,7 @@ task align_and_count {
148148
Int topNHits = 3
149149

150150
Int? machine_mem_gb
151-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
151+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
152152
}
153153

154154
String reads_basename=basename(reads_bam, ".bam")
@@ -191,7 +191,7 @@ task align_and_count_summary {
191191

192192
String output_prefix="count_summary"
193193

194-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
194+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
195195
}
196196

197197
command {
@@ -222,7 +222,7 @@ task aggregate_metagenomics_reports {
222222
String aggregate_taxlevel_focus = "species"
223223
Int aggregate_top_N_hits = 5
224224

225-
String docker="quay.io/broadinstitute/viral-classify:2.1.10.0"
225+
String docker="quay.io/broadinstitute/viral-classify:2.1.12.0"
226226
}
227227

228228
parameter_meta {
@@ -365,7 +365,7 @@ task tsv_join {
365365
String join_type="inner"
366366
String out_basename
367367

368-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
368+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
369369
}
370370

371371
command {
@@ -406,7 +406,7 @@ task tsv_stack {
406406
input {
407407
Array[File]+ input_tsvs
408408
String out_basename
409-
String docker="quay.io/broadinstitute/viral-core:2.1.10"
409+
String docker="quay.io/broadinstitute/viral-core:2.1.12"
410410
}
411411

412412
command {
@@ -436,7 +436,7 @@ task compare_two_genomes {
436436
File genome_two
437437
String out_basename
438438

439-
String docker="quay.io/broadinstitute/viral-assemble:2.1.10.0"
439+
String docker="quay.io/broadinstitute/viral-assemble:2.1.12.0"
440440
}
441441

442442
command {

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