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mass update of upstream docker tags #505

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merged 6 commits into from
Jan 5, 2024
Merged

mass update of upstream docker tags #505

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b29be04
update docker image tags for many dependencies
dpark01 Dec 21, 2023
3f2ab8d
so... we align more reads now by upgrading
dpark01 Dec 21, 2023
eca6df6
upgrade = magically better performance
dpark01 Dec 21, 2023
74a4b3a
bump ncbi-tools docker too
dpark01 Dec 22, 2023
b23d320
uh oh, running out of disk space
dpark01 Jan 5, 2024
0abb026
revert ncbi-tools docker update
dpark01 Jan 5, 2024
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14 changes: 14 additions & 0 deletions .github/workflows/build.yml
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Expand Up @@ -210,6 +210,13 @@ jobs:
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: clean up disk space
shell: bash
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: install java
uses: actions/setup-java@v3
with:
Expand Down Expand Up @@ -258,6 +265,13 @@ jobs:
fi
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
- name: clean up disk space
shell: bash
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: install python
uses: actions/setup-python@v4
with:
Expand Down
4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_assembly.wdl
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Expand Up @@ -431,7 +431,7 @@ task align_reads {
Boolean? skip_mark_dupes = false

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"

String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
}
Expand Down Expand Up @@ -827,7 +827,7 @@ task run_discordance {
String out_basename = "run"
Int min_coverage = 4

String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}
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:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

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:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

parameter_meta {
Expand Down
2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_interhost.wdl
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Expand Up @@ -351,7 +351,7 @@ task index_ref {
File? novocraft_license

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

Int disk_size = 100
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16 changes: 8 additions & 8 deletions pipes/WDL/tasks/tasks_metagenomics.wdl
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Expand Up @@ -11,7 +11,7 @@ task krakenuniq {
File krona_taxonomy_db_tgz # taxonomy.tab

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0" #skip-global-version-pin
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0" #skip-global-version-pin
}

Int disk_size = 750
Expand Down Expand Up @@ -143,7 +143,7 @@ task build_krakenuniq_db {
Int? zstd_compression_level

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0" #skip-global-version-pin
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0" #skip-global-version-pin
}

Int disk_size = 750
Expand Down Expand Up @@ -213,7 +213,7 @@ task kraken2 {
Int? min_base_qual

Int machine_mem_gb = 72
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0"
}

parameter_meta {
Expand Down Expand Up @@ -348,7 +348,7 @@ task build_kraken2_db {
Int? zstd_compression_level

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0"
}

Int disk_size = 750
Expand Down Expand Up @@ -490,7 +490,7 @@ task blastx {
File krona_taxonomy_db_tgz

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0"
}

parameter_meta {
Expand Down Expand Up @@ -580,7 +580,7 @@ task krona {
Int? magnitude_column

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0"
}

Int disk_size = 50
Expand Down Expand Up @@ -687,7 +687,7 @@ task filter_bam_to_taxa {
String out_filename_suffix = "filtered"

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0"
}

String out_basename = basename(classified_bam, ".bam") + "." + out_filename_suffix
Expand Down Expand Up @@ -774,7 +774,7 @@ task kaiju {
File krona_taxonomy_db_tgz # taxonomy/taxonomy.tab

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0"
}

String input_basename = basename(reads_unmapped_bam, ".bam")
Expand Down
10 changes: 5 additions & 5 deletions pipes/WDL/tasks/tasks_ncbi.wdl
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Expand Up @@ -192,7 +192,7 @@ task structured_comments {

File? filter_to_ids

String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}
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:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}
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:2.1.33"
String docker="quay.io/broadinstitute/viral-core:2.2.4"
}
Int disk_size = 100
parameter_meta {
Expand Down Expand Up @@ -896,7 +896,7 @@ task package_sc2_genbank_ftp_submission {
String spuid_namespace
String account_name

String docker = "quay.io/broadinstitute/viral-baseimage:0.1.20"
String docker = "quay.io/broadinstitute/viral-baseimage:0.2.0"
}
command <<<
set -e
Expand Down Expand Up @@ -960,7 +960,7 @@ task vadr {
File genome_fasta
String vadr_opts = "--glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn"

String docker = "quay.io/staphb/vadr:1.5.1"
String docker = "quay.io/staphb/vadr:1.6.3"
Int minlen = 50
Int maxlen = 30000
Int mem_size = 4
Expand Down
8 changes: 4 additions & 4 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
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Expand Up @@ -14,7 +14,7 @@ task nextclade_one_sample {
File? virus_properties
String? dataset_name
Int disk_size = 50
String docker = "nextstrain/nextclade:2.12.0"
String docker = "nextstrain/nextclade:2.14.0"
}
String basename = basename(genome_fasta, ".fasta")
command {
Expand Down Expand Up @@ -101,7 +101,7 @@ task nextclade_many_samples {
String basename
File? genome_ids_setdefault_blank
Int disk_size = 150
String docker = "nextstrain/nextclade:2.12.0"
String docker = "nextstrain/nextclade:2.14.0"
}
command <<<
set -e
Expand Down Expand Up @@ -280,7 +280,7 @@ task derived_cols {
String? lab_highlight_loc
Array[File] table_map = []

String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
Int disk_size = 50
}
parameter_meta {
Expand Down Expand Up @@ -848,7 +848,7 @@ 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-20211012T204409Z"
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
Int disk_size = 750
}
parameter_meta {
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:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}
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:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}
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:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

Int disk_size = 750
Expand Down Expand Up @@ -244,7 +244,7 @@ task rmdup_ubam {
String method = "mvicuna"

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

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:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

Int disk_size = 750
Expand Down Expand Up @@ -366,7 +366,7 @@ task FastqToUBAM {
String platform_name
String? sequencing_center

String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}
Int disk_size = 375
parameter_meta {
Expand Down Expand Up @@ -416,7 +416,7 @@ task read_depths {
File aligned_bam

String out_basename = basename(aligned_bam, '.bam')
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}
Int disk_size = 200
command <<<
Expand Down
14 changes: 7 additions & 7 deletions pipes/WDL/tasks/tasks_reports.wdl
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Expand Up @@ -15,7 +15,7 @@ task alignment_metrics {
Int? max_amplicons=500

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

String out_basename = basename(aligned_bam, ".bam")
Expand Down Expand Up @@ -131,7 +131,7 @@ task plot_coverage {
String? plotXLimits # of the form "min max" (ints, space between)
String? plotYLimits # of the form "min max" (ints, space between)

String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

Int disk_size = 375
Expand Down Expand Up @@ -278,7 +278,7 @@ task coverage_report {
Array[File] mapped_bam_idx # optional.. speeds it up if you provide it, otherwise we auto-index
String out_report_name = "coverage_report.txt"

String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

Int disk_size = 375
Expand Down Expand Up @@ -345,7 +345,7 @@ task fastqc {
input {
File reads_bam

String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}
parameter_meta {
reads_bam:{
Expand Down Expand Up @@ -388,7 +388,7 @@ task align_and_count {
Int topNHits = 3

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

String reads_basename=basename(reads_bam, ".bam")
Expand Down Expand Up @@ -448,7 +448,7 @@ task align_and_count_summary {

String output_prefix = "count_summary"

String docker = "quay.io/broadinstitute/viral-core:2.1.33"
String docker = "quay.io/broadinstitute/viral-core:2.2.4"
}

Int disk_size = 100
Expand Down Expand Up @@ -483,7 +483,7 @@ task aggregate_metagenomics_reports {
String aggregate_taxlevel_focus = "species"
Int aggregate_top_N_hits = 5

String docker = "quay.io/broadinstitute/viral-classify:2.1.33.0"
String docker = "quay.io/broadinstitute/viral-classify:2.2.3.0"
}

parameter_meta {
Expand Down
4 changes: 2 additions & 2 deletions pipes/WDL/tasks/tasks_sarscov2.wdl
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Expand Up @@ -10,7 +10,7 @@ task pangolin_one_sample {
Float? max_ambig
String? analysis_mode
Boolean update_dbs_now=false
String docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.22"
String docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.23.1"
}
String basename = basename(genome_fasta, ".fasta")
Int disk_size = 50
Expand Down Expand Up @@ -93,7 +93,7 @@ task pangolin_many_samples {
String? analysis_mode
Boolean update_dbs_now=false
String basename
String docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.22"
String docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.23.1"
}
Int disk_size = 100
command <<<
Expand Down
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