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bump upstream docker images #556

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merged 10 commits into from
Sep 23, 2024
Merged

bump upstream docker images #556

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42dca48
bump viral-core to 2.3.4 and viral-assembly to 2.3.4.0
dpark01 Sep 18, 2024
8b65adc
bump viral-core to 2.3.5
dpark01 Sep 19, 2024
2c551cd
bump viral-assemble 2.3.4.0 to 2.3.5.0
dpark01 Sep 19, 2024
daa1fbd
Merge remote-tracking branch 'origin/master' into dp-bump-core
dpark01 Sep 19, 2024
033966b
santize fasta header before running metrics
dpark01 Sep 19, 2024
3998d28
update viral-core, viral-assemble, viral-phylo to 2.3.6, 2.3.6.0, 2.3…
dpark01 Sep 20, 2024
4d745f1
Merge remote-tracking branch 'origin/master' into dp-bump-core
dpark01 Sep 20, 2024
ae5a446
lofreq handle spaces in fasta
dpark01 Sep 20, 2024
acfd1d4
bump viral-assemble
dpark01 Sep 20, 2024
a241e1f
bump requirements-modules oops
dpark01 Sep 20, 2024
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14 changes: 7 additions & 7 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ task assemble {
String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt")

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
}
parameter_meta{
reads_unmapped_bam: {
Expand Down Expand Up @@ -115,7 +115,7 @@ task select_references {
Int? skani_s
Int? skani_c

String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
Int machine_mem_gb = 4
Int cpu = 2
Int disk_size = 100
Expand Down Expand Up @@ -206,7 +206,7 @@ task scaffold {
Float? scaffold_min_pct_contig_aligned

Int? machine_mem_gb
String docker="quay.io/broadinstitute/viral-assemble:2.3.2.0"
String docker="quay.io/broadinstitute/viral-assemble:2.3.6.1"

# do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
String sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades")
Expand Down Expand Up @@ -583,7 +583,7 @@ task align_reads {
Boolean skip_mark_dupes = false

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"

String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
}
Expand Down Expand Up @@ -720,7 +720,7 @@ task refine_assembly_with_aligned_reads {
Int min_coverage = 3

Int machine_mem_gb = 15
String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
}

Int disk_size = 375
Expand Down Expand Up @@ -845,7 +845,7 @@ task refine_2x_and_plot {
String? plot_coverage_novoalign_options = "-r Random -l 40 -g 40 -x 20 -t 100 -k"

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"

# do this in two steps in case the input doesn't actually have "cleaned" in the name
String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned")
Expand Down Expand Up @@ -981,7 +981,7 @@ task run_discordance {
String out_basename = "run"
Int min_coverage = 4

String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}
parameter_meta {
reads_aligned_bam: {
Expand Down
4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_demux.wdl
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Expand Up @@ -6,7 +6,7 @@ task merge_tarballs {
String out_filename

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}

Int disk_size = 2625
Expand Down Expand Up @@ -163,7 +163,7 @@ task illumina_demux {

Int? machine_mem_gb
Int disk_size = 2625
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}

parameter_meta {
Expand Down
8 changes: 4 additions & 4 deletions pipes/WDL/tasks/tasks_interhost.wdl
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Expand Up @@ -160,7 +160,7 @@ task multi_align_mafft_ref {
Float? mafft_gapOpeningPenalty

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
}

String fasta_basename = basename(reference_fasta, '.fasta')
Expand Down Expand Up @@ -207,7 +207,7 @@ task multi_align_mafft {
Float? mafft_gapOpeningPenalty

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
}

Int disk_size = 200
Expand Down Expand Up @@ -351,7 +351,7 @@ task index_ref {
File? novocraft_license

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}

Int disk_size = 100
Expand Down Expand Up @@ -476,7 +476,7 @@ task merge_vcfs_gatk {
File ref_fasta

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

String output_prefix = "merged"
}
Expand Down
15 changes: 10 additions & 5 deletions pipes/WDL/tasks/tasks_intrahost.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ task lofreq {
File reference_fasta

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

# make local copies because CWD is writeable but localization dir isn't always
cp "~{reference_fasta}" reference.fasta
cp "~{aligned_bam}" aligned.bam
python3<<CODE
import shutil
import util.file
with util.file.fastas_with_sanitized_ids("~{reference_fasta}", use_tmp=True) as sanitized_fastas:
shutil.copyfile(sanitized_fastas[0], 'reference.fasta')
CODE

# samtools faidx fails if fasta is empty
if [ $(grep -v '^>' reference.fasta | tr -d '\nNn' | wc -c) == "0" ]; then
Expand Down Expand Up @@ -191,7 +196,7 @@ task isnvs_per_sample {
Boolean removeDoublyMappedReads = true

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

String sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped")
}
Expand Down Expand Up @@ -234,7 +239,7 @@ task isnvs_vcf {
Boolean naiveFilter = false

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
}

parameter_meta {
Expand Down Expand Up @@ -308,7 +313,7 @@ task annotate_vcf_snpeff {
String? emailAddress

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

String output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
}
Expand Down
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_megablast.wdl
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Expand Up @@ -15,7 +15,7 @@ task trim_rmdup_subsamp {
Int cpu = 16
Int disk_size_gb = 100

String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
}

parameter_meta {
Expand Down
18 changes: 9 additions & 9 deletions pipes/WDL/tasks/tasks_ncbi.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ task download_fasta {
Array[String]+ accessions
String emailAddress

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

command {
Expand Down Expand Up @@ -38,7 +38,7 @@ task download_annotations {
String emailAddress
String combined_out_prefix

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

command <<<
Expand Down Expand Up @@ -85,7 +85,7 @@ task annot_transfer {
File reference_fasta
Array[File]+ reference_feature_table

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

parameter_meta {
Expand Down Expand Up @@ -139,7 +139,7 @@ task align_and_annot_transfer_single {
Array[File]+ reference_fastas
Array[File]+ reference_feature_tables

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

parameter_meta {
Expand Down Expand Up @@ -192,7 +192,7 @@ task structured_comments {

File? filter_to_ids

String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}
String out_base = basename(assembly_stats_tsv, '.txt')
command <<<
Expand Down Expand Up @@ -272,7 +272,7 @@ task rename_fasta_header {

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

String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}
command {
set -e
Expand Down Expand Up @@ -437,7 +437,7 @@ task sra_meta_prep {
Boolean paired

String out_name = "sra_metadata.tsv"
String docker="quay.io/broadinstitute/viral-core:2.3.2"
String docker="quay.io/broadinstitute/viral-core:2.3.6"
}
Int disk_size = 100
parameter_meta {
Expand Down Expand Up @@ -653,7 +653,7 @@ task biosample_to_genbank {
File? filter_to_ids

Boolean s_dropout_note = true
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
}
String base = basename(biosample_attributes, ".txt")
command {
Expand Down Expand Up @@ -851,7 +851,7 @@ task prepare_genbank {
String? assembly_method_version

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
}

parameter_meta {
Expand Down
8 changes: 4 additions & 4 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
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Expand Up @@ -321,7 +321,7 @@ task derived_cols {
String? lab_highlight_loc
Array[File] table_map = []

String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
Int disk_size = 50
}
parameter_meta {
Expand Down Expand Up @@ -889,7 +889,7 @@ task filter_sequences_to_list {

String out_fname = sub(sub(basename(sequences, ".zst"), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
# Prior docker image: "nextstrain/base:build-20240318T173028Z"
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
Int disk_size = 750
}
parameter_meta {
Expand Down Expand Up @@ -990,7 +990,7 @@ task mafft_one_chr {
Boolean large = false
Boolean memsavetree = false

String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
Int mem_size = 500
Int cpus = 64
Int disk_size = 750
Expand Down Expand Up @@ -1078,7 +1078,7 @@ task mafft_one_chr_chunked {
Int batch_chunk_size = 2000
Int threads_per_job = 2

String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
String docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
Int mem_size = 32
Int cpus = 64
Int disk_size = 750
Expand Down
14 changes: 7 additions & 7 deletions pipes/WDL/tasks/tasks_read_utils.wdl
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Expand Up @@ -84,7 +84,7 @@ task group_bams_by_sample {
task get_bam_samplename {
input {
File bam
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}
Int disk_size = round(size(bam, "GB")) + 50
command <<<
Expand All @@ -111,7 +111,7 @@ task get_sample_meta {
input {
Array[File] samplesheets_extended

String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}
Int disk_size = 50
command <<<
Expand Down Expand Up @@ -172,7 +172,7 @@ task merge_and_reheader_bams {
File? reheader_table
String out_basename = basename(in_bams[0], ".bam")

String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
Int disk_size = 750
Int machine_mem_gb = 4
}
Expand Down Expand Up @@ -244,7 +244,7 @@ task rmdup_ubam {
String method = "mvicuna"

Int machine_mem_gb = 7
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}

Int disk_size = 375
Expand Down Expand Up @@ -303,7 +303,7 @@ task downsample_bams {
Boolean deduplicateAfter = false

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}

Int disk_size = 750
Expand Down Expand Up @@ -367,7 +367,7 @@ task FastqToUBAM {
String? sequencing_center
String? additional_picard_options

String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}
Int disk_size = 375
parameter_meta {
Expand Down Expand Up @@ -418,7 +418,7 @@ task read_depths {
File aligned_bam

String out_basename = basename(aligned_bam, '.bam')
String docker = "quay.io/broadinstitute/viral-core:2.3.2"
String docker = "quay.io/broadinstitute/viral-core:2.3.6"
}
Int disk_size = 200
command <<<
Expand Down
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