Skip to content

Commit cc8a4b7

Browse files
dpark01dpark01
authored
Merge pull request #556 from broadinstitute/dp-bump-core
bump upstream docker images
2 parents 4179ee0 + a241e1f commit cc8a4b7

13 files changed

+66
-56
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:2.3.2.0"
18+
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
1919
}
2020
parameter_meta{
2121
reads_unmapped_bam: {
@@ -115,7 +115,7 @@ task select_references {
115115
Int? skani_s
116116
Int? skani_c
117117

118-
String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
118+
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
119119
Int machine_mem_gb = 4
120120
Int cpu = 2
121121
Int disk_size = 100
@@ -206,7 +206,7 @@ task scaffold {
206206
Float? scaffold_min_pct_contig_aligned
207207
208208
Int? machine_mem_gb
209-
String docker="quay.io/broadinstitute/viral-assemble:2.3.2.0"
209+
String docker="quay.io/broadinstitute/viral-assemble:2.3.6.1"
210210
211211
# do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
212212
String sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades")
@@ -583,7 +583,7 @@ task align_reads {
583583
Boolean skip_mark_dupes = false
584584
585585
Int? machine_mem_gb
586-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
586+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
587587
588588
String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
589589
}
@@ -720,7 +720,7 @@ task refine_assembly_with_aligned_reads {
720720
Int min_coverage = 3
721721
722722
Int machine_mem_gb = 15
723-
String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
723+
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
724724
}
725725
726726
Int disk_size = 375
@@ -845,7 +845,7 @@ task refine_2x_and_plot {
845845
String? plot_coverage_novoalign_options = "-r Random -l 40 -g 40 -x 20 -t 100 -k"
846846
847847
Int? machine_mem_gb
848-
String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
848+
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
849849
850850
# do this in two steps in case the input doesn't actually have "cleaned" in the name
851851
String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned")
@@ -981,7 +981,7 @@ task run_discordance {
981981
String out_basename = "run"
982982
Int min_coverage = 4
983983
984-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
984+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
985985
}
986986
parameter_meta {
987987
reads_aligned_bam: {

‎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:2.3.2"
9+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
1010
}
1111

1212
Int disk_size = 2625
@@ -163,7 +163,7 @@ task illumina_demux {
163163
164164
Int? machine_mem_gb
165165
Int disk_size = 2625
166-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
166+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
167167
}
168168
169169
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-phylo:2.1.20.2"
163+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
164164
}
165165

166166
String fasta_basename = basename(reference_fasta, '.fasta')
@@ -207,7 +207,7 @@ task multi_align_mafft {
207207
Float? mafft_gapOpeningPenalty
208208

209209
Int? machine_mem_gb
210-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
210+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
211211
}
212212

213213
Int disk_size = 200
@@ -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:2.3.2"
354+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
355355
}
356356

357357
Int disk_size = 100
@@ -476,7 +476,7 @@ task merge_vcfs_gatk {
476476
File ref_fasta
477477

478478
Int? machine_mem_gb
479-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
479+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
480480

481481
String output_prefix = "merged"
482482
}

‎pipes/WDL/tasks/tasks_intrahost.wdl

Lines changed: 10 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -136,7 +136,7 @@ task lofreq {
136136
File reference_fasta
137137

138138
String out_basename = basename(aligned_bam, '.bam')
139-
String docker = "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
139+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
140140
}
141141
Int disk_size = 200
142142
command <<<
@@ -145,8 +145,13 @@ task lofreq {
145145
lofreq version | grep version | sed 's/.* \(.*\)/\1/g' | tee LOFREQ_VERSION
146146

147147
# make local copies because CWD is writeable but localization dir isn't always
148-
cp "~{reference_fasta}" reference.fasta
149148
cp "~{aligned_bam}" aligned.bam
149+
python3<<CODE
150+
import shutil
151+
import util.file
152+
with util.file.fastas_with_sanitized_ids("~{reference_fasta}", use_tmp=True) as sanitized_fastas:
153+
shutil.copyfile(sanitized_fastas[0], 'reference.fasta')
154+
CODE
150155
151156
# samtools faidx fails if fasta is empty
152157
if [ $(grep -v '^>' reference.fasta | tr -d '\nNn' | wc -c) == "0" ]; then
@@ -191,7 +196,7 @@ task isnvs_per_sample {
191196
Boolean removeDoublyMappedReads = true
192197
193198
Int? machine_mem_gb
194-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
199+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
195200
196201
String sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped")
197202
}
@@ -234,7 +239,7 @@ task isnvs_vcf {
234239
Boolean naiveFilter = false
235240
236241
Int? machine_mem_gb
237-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
242+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
238243
}
239244
240245
parameter_meta {
@@ -308,7 +313,7 @@ task annotate_vcf_snpeff {
308313
String? emailAddress
309314
310315
Int? machine_mem_gb
311-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
316+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
312317
313318
String output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
314319
}

‎pipes/WDL/tasks/tasks_megablast.wdl

Lines changed: 1 addition & 1 deletion
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-assemble:2.3.2.0"
18+
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
1919
}
2020

2121
parameter_meta {

‎pipes/WDL/tasks/tasks_ncbi.wdl

Lines changed: 9 additions & 9 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-phylo:2.1.20.2"
9+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
1010
}
1111

1212
command {
@@ -38,7 +38,7 @@ task download_annotations {
3838
String emailAddress
3939
String combined_out_prefix
4040

41-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
41+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
4242
}
4343

4444
command <<<
@@ -85,7 +85,7 @@ task annot_transfer {
8585
File reference_fasta
8686
Array[File]+ reference_feature_table
8787

88-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
88+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
8989
}
9090

9191
parameter_meta {
@@ -139,7 +139,7 @@ task align_and_annot_transfer_single {
139139
Array[File]+ reference_fastas
140140
Array[File]+ reference_feature_tables
141141

142-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
142+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
143143
}
144144

145145
parameter_meta {
@@ -192,7 +192,7 @@ task structured_comments {
192192

193193
File? filter_to_ids
194194

195-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
195+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
196196
}
197197
String out_base = basename(assembly_stats_tsv, '.txt')
198198
command <<<
@@ -272,7 +272,7 @@ task rename_fasta_header {
272272
273273
String out_basename = basename(genome_fasta, ".fasta")
274274
275-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
275+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
276276
}
277277
command {
278278
set -e
@@ -437,7 +437,7 @@ task sra_meta_prep {
437437
Boolean paired
438438
439439
String out_name = "sra_metadata.tsv"
440-
String docker="quay.io/broadinstitute/viral-core:2.3.2"
440+
String docker="quay.io/broadinstitute/viral-core:2.3.6"
441441
}
442442
Int disk_size = 100
443443
parameter_meta {
@@ -653,7 +653,7 @@ task biosample_to_genbank {
653653
File? filter_to_ids
654654
655655
Boolean s_dropout_note = true
656-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
656+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
657657
}
658658
String base = basename(biosample_attributes, ".txt")
659659
command {
@@ -851,7 +851,7 @@ task prepare_genbank {
851851
String? assembly_method_version
852852
853853
Int? machine_mem_gb
854-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
854+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
855855
}
856856
857857
parameter_meta {

‎pipes/WDL/tasks/tasks_nextstrain.wdl

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -321,7 +321,7 @@ task derived_cols {
321321
String? lab_highlight_loc
322322
Array[File] table_map = []
323323
324-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
324+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
325325
Int disk_size = 50
326326
}
327327
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-core:2.3.2"
892+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
893893
Int disk_size = 750
894894
}
895895
parameter_meta {
@@ -990,7 +990,7 @@ task mafft_one_chr {
990990
Boolean large = false
991991
Boolean memsavetree = false
992992
993-
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
993+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
994994
Int mem_size = 500
995995
Int cpus = 64
996996
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-phylo:2.1.20.2"
1081+
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
10821082
Int mem_size = 32
10831083
Int cpus = 64
10841084
Int disk_size = 750

‎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:2.3.2"
87+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
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:2.3.2"
114+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
115115
}
116116
Int disk_size = 50
117117
command <<<
@@ -172,7 +172,7 @@ task merge_and_reheader_bams {
172172
File? reheader_table
173173
String out_basename = basename(in_bams[0], ".bam")
174174
175-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
175+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
176176
Int disk_size = 750
177177
Int machine_mem_gb = 4
178178
}
@@ -244,7 +244,7 @@ task rmdup_ubam {
244244
String method = "mvicuna"
245245
246246
Int machine_mem_gb = 7
247-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
247+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
248248
}
249249
250250
Int disk_size = 375
@@ -303,7 +303,7 @@ task downsample_bams {
303303
Boolean deduplicateAfter = false
304304
305305
Int? machine_mem_gb
306-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
306+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
307307
}
308308
309309
Int disk_size = 750
@@ -367,7 +367,7 @@ task FastqToUBAM {
367367
String? sequencing_center
368368
String? additional_picard_options
369369
370-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
370+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
371371
}
372372
Int disk_size = 375
373373
parameter_meta {
@@ -418,7 +418,7 @@ task read_depths {
418418
File aligned_bam
419419
420420
String out_basename = basename(aligned_bam, '.bam')
421-
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
421+
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
422422
}
423423
Int disk_size = 200
424424
command <<<

0 commit comments

Comments
 (0)