From d65572664bd3694af1b7583067e1282a29f60f9f Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Tue, 5 Nov 2024 12:38:03 -0500 Subject: [PATCH] update viral-core 2.3.6 -> 2.4.0 (#566) update viral-core 2.3.6 -> 2.4.0 so the NCBI datasets CLI tools are available --- pipes/WDL/tasks/tasks_assembly.wdl | 4 ++-- pipes/WDL/tasks/tasks_demux.wdl | 4 ++-- pipes/WDL/tasks/tasks_interhost.wdl | 2 +- pipes/WDL/tasks/tasks_megablast.wdl | 2 +- pipes/WDL/tasks/tasks_ncbi.wdl | 6 +++--- pipes/WDL/tasks/tasks_nextstrain.wdl | 4 ++-- pipes/WDL/tasks/tasks_read_utils.wdl | 14 +++++++------- pipes/WDL/tasks/tasks_reports.wdl | 12 ++++++------ pipes/WDL/tasks/tasks_taxon_filter.wdl | 2 +- pipes/WDL/tasks/tasks_terra.wdl | 2 +- pipes/WDL/tasks/tasks_utils.wdl | 8 ++++---- requirements-modules.txt | 2 +- 12 files changed, 31 insertions(+), 31 deletions(-) diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl index 4b7a5abbc..7d577bd4b 100644 --- a/pipes/WDL/tasks/tasks_assembly.wdl +++ b/pipes/WDL/tasks/tasks_assembly.wdl @@ -583,7 +583,7 @@ task align_reads { Boolean skip_mark_dupes = false Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" String sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean") } @@ -981,7 +981,7 @@ task run_discordance { String out_basename = "run" Int min_coverage = 4 - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } parameter_meta { reads_aligned_bam: { diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl index e3aa8b01d..86d209970 100644 --- a/pipes/WDL/tasks/tasks_demux.wdl +++ b/pipes/WDL/tasks/tasks_demux.wdl @@ -6,7 +6,7 @@ task merge_tarballs { String out_filename Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 2625 @@ -163,7 +163,7 @@ task illumina_demux { Int? machine_mem_gb Int disk_size = 2625 - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } parameter_meta { diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl index c3df6e451..93e875dba 100644 --- a/pipes/WDL/tasks/tasks_interhost.wdl +++ b/pipes/WDL/tasks/tasks_interhost.wdl @@ -351,7 +351,7 @@ task index_ref { File? novocraft_license Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 100 diff --git a/pipes/WDL/tasks/tasks_megablast.wdl b/pipes/WDL/tasks/tasks_megablast.wdl index b4ad19a15..d93a359c1 100755 --- a/pipes/WDL/tasks/tasks_megablast.wdl +++ b/pipes/WDL/tasks/tasks_megablast.wdl @@ -36,7 +36,7 @@ task trim_rmdup_subsamp { command <<< set -ex o pipefail assembly.py --version | tee VERSION - #BAM ->FASTQ-> OutBam? https://github.com/broadinstitute/viral-assemble/blob/80bcc1da5c6a0174362ca9fd8bc0b49ee0b4103b/assembly.py#L91 + #BAM ->FASTQ-> OutBam? https://github.com/broadinstitute/viral-assemble:2.3.6.1 assembly.py trim_rmdup_subsamp \ "~{inBam}" \ "~{clipDb}" \ diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl index 0e4511a5e..31278f662 100644 --- a/pipes/WDL/tasks/tasks_ncbi.wdl +++ b/pipes/WDL/tasks/tasks_ncbi.wdl @@ -192,7 +192,7 @@ task structured_comments { File? filter_to_ids - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } String out_base = basename(assembly_stats_tsv, '.txt') command <<< @@ -272,7 +272,7 @@ task rename_fasta_header { String out_basename = basename(genome_fasta, ".fasta") - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } command { set -e @@ -437,7 +437,7 @@ task sra_meta_prep { Boolean paired String out_name = "sra_metadata.tsv" - String docker="quay.io/broadinstitute/viral-core:2.3.6" + String docker="quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 100 parameter_meta { diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 593c5ce20..52d874982 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -321,7 +321,7 @@ task derived_cols { String? lab_highlight_loc Array[File] table_map = [] - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" Int disk_size = 50 } parameter_meta { @@ -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:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" Int disk_size = 750 } parameter_meta { diff --git a/pipes/WDL/tasks/tasks_read_utils.wdl b/pipes/WDL/tasks/tasks_read_utils.wdl index e7060b5cd..ce72165e2 100644 --- a/pipes/WDL/tasks/tasks_read_utils.wdl +++ b/pipes/WDL/tasks/tasks_read_utils.wdl @@ -84,7 +84,7 @@ task group_bams_by_sample { task get_bam_samplename { input { File bam - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = round(size(bam, "GB")) + 50 command <<< @@ -111,7 +111,7 @@ task get_sample_meta { input { Array[File] samplesheets_extended - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 50 command <<< @@ -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:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" Int disk_size = 750 Int machine_mem_gb = 4 } @@ -244,7 +244,7 @@ task rmdup_ubam { String method = "mvicuna" Int machine_mem_gb = 7 - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 375 @@ -303,7 +303,7 @@ task downsample_bams { Boolean deduplicateAfter = false Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 750 @@ -367,7 +367,7 @@ task FastqToUBAM { String? sequencing_center String? additional_picard_options - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 375 parameter_meta { @@ -418,7 +418,7 @@ task read_depths { File aligned_bam String out_basename = basename(aligned_bam, '.bam') - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 200 command <<< diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl index f9cda58f5..146915b44 100644 --- a/pipes/WDL/tasks/tasks_reports.wdl +++ b/pipes/WDL/tasks/tasks_reports.wdl @@ -15,7 +15,7 @@ task alignment_metrics { Int max_amplicons=500 Int machine_mem_gb=32 - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } String out_basename = basename(aligned_bam, ".bam") @@ -142,7 +142,7 @@ 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:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 375 @@ -289,7 +289,7 @@ 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:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 375 @@ -356,7 +356,7 @@ task fastqc { input { File reads_bam - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } parameter_meta { reads_bam:{ @@ -404,7 +404,7 @@ task align_and_count { Boolean keep_duplicates_when_filtering = false Int? machine_mem_gb - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } String reads_basename=basename(reads_bam, ".bam") @@ -516,7 +516,7 @@ task align_and_count_summary { String output_prefix = "count_summary" - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 100 diff --git a/pipes/WDL/tasks/tasks_taxon_filter.wdl b/pipes/WDL/tasks/tasks_taxon_filter.wdl index 95a2869ba..9b1ff62fc 100644 --- a/pipes/WDL/tasks/tasks_taxon_filter.wdl +++ b/pipes/WDL/tasks/tasks_taxon_filter.wdl @@ -211,7 +211,7 @@ task merge_one_per_sample { Boolean rmdup = false Int machine_mem_gb = 7 - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 750 diff --git a/pipes/WDL/tasks/tasks_terra.wdl b/pipes/WDL/tasks/tasks_terra.wdl index 627e592da..a920ad548 100644 --- a/pipes/WDL/tasks/tasks_terra.wdl +++ b/pipes/WDL/tasks/tasks_terra.wdl @@ -391,7 +391,7 @@ task create_or_update_sample_tables { String sample_table_name = "sample" String library_table_name = "library" - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } meta { diff --git a/pipes/WDL/tasks/tasks_utils.wdl b/pipes/WDL/tasks/tasks_utils.wdl index 4bd6edaf8..a527d5607 100644 --- a/pipes/WDL/tasks/tasks_utils.wdl +++ b/pipes/WDL/tasks/tasks_utils.wdl @@ -103,7 +103,7 @@ task zcat { { if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES >>> runtime { - docker: "quay.io/broadinstitute/viral-core:2.3.6" + docker: "quay.io/broadinstitute/viral-core:2.4.0" memory: "1 GB" cpu: cpus disks: "local-disk " + disk_size + " LOCAL" @@ -430,7 +430,7 @@ task tsv_join { runtime { memory: "~{machine_mem_gb} GB" cpu: 4 - docker: "quay.io/broadinstitute/viral-core:2.3.6" + docker: "quay.io/broadinstitute/viral-core:2.4.0" disks: "local-disk " + disk_size + " HDD" disk: disk_size + " GB" # TES dx_instance_type: "mem1_ssd1_v2_x4" @@ -517,7 +517,7 @@ task tsv_stack { input { Array[File]+ input_tsvs String out_basename - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" } Int disk_size = 50 @@ -780,7 +780,7 @@ task filter_sequences_by_length { File sequences_fasta Int min_non_N = 1 - String docker = "quay.io/broadinstitute/viral-core:2.3.6" + String docker = "quay.io/broadinstitute/viral-core:2.4.0" Int disk_size = 750 } parameter_meta { diff --git a/requirements-modules.txt b/requirements-modules.txt index 3c569e8ca..0f66fa1a8 100644 --- a/requirements-modules.txt +++ b/requirements-modules.txt @@ -1,4 +1,4 @@ -broadinstitute/viral-core=2.3.6 +broadinstitute/viral-core=2.4.0 broadinstitute/viral-assemble=2.3.6.1 broadinstitute/viral-classify=2.2.4.2 broadinstitute/viral-phylo=2.3.6.0