diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl index 20a85f600..4b7a5abbc 100644 --- a/pipes/WDL/tasks/tasks_assembly.wdl +++ b/pipes/WDL/tasks/tasks_assembly.wdl @@ -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: { @@ -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 @@ -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") @@ -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") } @@ -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 @@ -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") @@ -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: { diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl index 9a63dc521..e3aa8b01d 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } parameter_meta { diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl index e8ca286ce..c3df6e451 100644 --- a/pipes/WDL/tasks/tasks_interhost.wdl +++ b/pipes/WDL/tasks/tasks_interhost.wdl @@ -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') @@ -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 @@ -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 @@ -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" } diff --git a/pipes/WDL/tasks/tasks_intrahost.wdl b/pipes/WDL/tasks/tasks_intrahost.wdl index 83dc49599..10eb1b4f1 100644 --- a/pipes/WDL/tasks/tasks_intrahost.wdl +++ b/pipes/WDL/tasks/tasks_intrahost.wdl @@ -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 <<< @@ -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<' reference.fasta | tr -d '\nNn' | wc -c) == "0" ]; then @@ -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") } @@ -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 { @@ -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") } diff --git a/pipes/WDL/tasks/tasks_megablast.wdl b/pipes/WDL/tasks/tasks_megablast.wdl index 7b9822545..b4ad19a15 100755 --- a/pipes/WDL/tasks/tasks_megablast.wdl +++ b/pipes/WDL/tasks/tasks_megablast.wdl @@ -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 { diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl index abb5a3d1d..0e4511a5e 100644 --- a/pipes/WDL/tasks/tasks_ncbi.wdl +++ b/pipes/WDL/tasks/tasks_ncbi.wdl @@ -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 { @@ -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 <<< @@ -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 { @@ -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 { @@ -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 <<< @@ -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 @@ -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 { @@ -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 { @@ -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 { diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 24d7023ea..5680b45db 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" Int disk_size = 750 } parameter_meta { @@ -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 @@ -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 diff --git a/pipes/WDL/tasks/tasks_read_utils.wdl b/pipes/WDL/tasks/tasks_read_utils.wdl index a42aad19e..e7060b5cd 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } Int disk_size = 750 @@ -367,7 +367,7 @@ task FastqToUBAM { String? sequencing_center String? additional_picard_options - String docker = "quay.io/broadinstitute/viral-core:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } Int disk_size = 200 command <<< diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl index 36205cb1b..f9cda58f5 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } String out_basename = basename(aligned_bam, ".bam") @@ -28,7 +28,12 @@ task alignment_metrics { echo "Requesting $MEM_MB MB of RAM for Java" # requisite Picard fasta indexing - cp "~{ref_fasta}" reference.fasta + python3< MEM_BYTES >>> runtime { - docker: "quay.io/broadinstitute/viral-core:2.3.2" + docker: "quay.io/broadinstitute/viral-core:2.3.6" 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:2.3.2" + docker: "quay.io/broadinstitute/viral-core:2.3.6" 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" } 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:2.3.2" + String docker = "quay.io/broadinstitute/viral-core:2.3.6" Int disk_size = 750 } parameter_meta { diff --git a/requirements-modules.txt b/requirements-modules.txt index ba97d6f92..845f418a7 100644 --- a/requirements-modules.txt +++ b/requirements-modules.txt @@ -1,7 +1,7 @@ -broadinstitute/viral-core=2.3.2 -broadinstitute/viral-assemble=2.3.2.0 +broadinstitute/viral-core=2.3.6 +broadinstitute/viral-assemble=2.3.6.1 broadinstitute/viral-classify=2.2.4.2 -broadinstitute/viral-phylo=2.1.20.2 +broadinstitute/viral-phylo=2.3.6.0 broadinstitute/py3-bio=0.1.2 broadinstitute/beast-beagle-cuda=1.10.5pre broadinstitute/ncbi-tools=2.10.7.10