diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index e6e628eba..8fb09ecd8 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -13,10 +13,10 @@ task nextclade_one_sample { File? pcr_primers_csv File? virus_properties String? dataset_name + Int disk_size = 50 String docker = "nextstrain/nextclade:2.12.0" } String basename = basename(genome_fasta, ".fasta") - Int disk_size = 50 command { set -e apt-get update @@ -100,9 +100,9 @@ task nextclade_many_samples { String? dataset_name String basename File? genome_ids_setdefault_blank + Int disk_size = 150 String docker = "nextstrain/nextclade:2.12.0" } - Int disk_size = 100 command <<< set -e apt-get update @@ -281,8 +281,8 @@ task derived_cols { Array[File] table_map = [] String docker = "quay.io/broadinstitute/viral-core:2.1.33" + Int disk_size = 50 } - Int disk_size = 50 parameter_meta { lab_highlight_loc: { description: "This option copies the 'originating_lab' and 'submitting_lab' columns to new ones including a prefix, but only if they match certain criteria. The value of this string must be of the form prefix;col_header=value:col_header=value. For example, 'MA;country=USA:division=Massachusetts' will copy the originating_lab and submitting_lab columns to MA_originating_lab and MA_submitting_lab, but only for those rows where country=USA and division=Massachusetts." @@ -391,12 +391,12 @@ task derived_cols { task filter_segments { input { File all_samples_fasta - Int? segment = 1 + Int segment = 1 File? pre_assembled_samples_fasta - Int? machine_mem_gb + Int machine_mem_gb = 3 + Int disk_size = 375 } - Int disk_size = 375 command <<< python3 <>> runtime { docker: "python:slim" - memory: select_first([machine_mem_gb, 3]) + " GB" + memory: machine_mem_gb + " GB" cpu: 1 disks: "local-disk " + disk_size + " LOCAL" disk: disk_size + " GB" # TES @@ -449,9 +449,10 @@ task nextstrain_build_subsample { File? keep_list File? drop_list - Int? machine_mem_gb + Int machine_mem_gb = 50 String docker = "nextstrain/base:build-20211012T204409Z" String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a" + Int disk_size = 750 } parameter_meta { alignment_msa_fasta: { @@ -474,7 +475,6 @@ task nextstrain_build_subsample { patterns: ["*.yaml"] } } - Int disk_size = 375 command <<< set -e -o pipefail augur version > VERSION @@ -570,7 +570,7 @@ task nextstrain_build_subsample { >>> runtime { docker: docker - memory: select_first([machine_mem_gb, 50]) + " GB" + memory: machine_mem_gb + " GB" cpu : 4 disks: "local-disk " + disk_size + " HDD" disk: disk_size + " GB" # TES @@ -595,8 +595,8 @@ task nextstrain_ncov_defaults { input { String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a" String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 50 } - Int disk_size = 50 command { set -e wget -q "https://github.com/nextstrain/ncov/archive/~{nextstrain_ncov_repo_commit}.tar.gz" @@ -633,10 +633,9 @@ task nextstrain_deduplicate_sequences { String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a" String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 } - Int disk_size = 375 - parameter_meta { sequences_fasta: { description: "FASTA file with multiple sequences", @@ -688,10 +687,9 @@ task nextstrain_ncov_sanitize_gisaid_data { String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a" String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 } - Int disk_size = 375 - parameter_meta { sequences_gisaid_fasta: { description: "Multiple sequences downloaded from GISAID", @@ -765,8 +763,8 @@ task filter_subsample_sequences { Array[String]? include_where String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 } - Int disk_size = 100 parameter_meta { sequences_fasta: { description: "Set of sequences (unaligned fasta or aligned fasta -- one sequence per genome) or variants (vcf format) to subsample using augur filter.", @@ -850,8 +848,8 @@ task filter_sequences_to_list { String out_fname = sub(sub(basename(sequences), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta") String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 } - Int disk_size = 200 parameter_meta { sequences: { description: "Set of sequences (unaligned fasta or aligned fasta -- one sequence per genome) or variants (vcf format) to subsample using augur filter.", @@ -952,8 +950,8 @@ task mafft_one_chr { String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2" Int mem_size = 500 Int cpus = 64 + Int disk_size = 750 } - Int disk_size = 750 command <<< set -e @@ -1039,9 +1037,9 @@ task mafft_one_chr_chunked { String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2" Int mem_size = 32 - Int cpus = 96 + Int cpus = 64 + Int disk_size = 750 } - Int disk_size = 750 command <<< set -e @@ -1146,8 +1144,8 @@ task augur_mafft_align { Boolean remove_reference = true String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 } - Int disk_size = 750 command <<< set -e augur version > VERSION @@ -1187,9 +1185,9 @@ task snp_sites { File msa_fasta Boolean allow_wildcard_bases = true String docker = "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0" + Int disk_size = 750 } String out_basename = basename(msa_fasta, ".fasta") - Int disk_size = 100 command { snp-sites -V > VERSION snp-sites -v ~{true="" false="-c" allow_wildcard_bases} -o "~{out_basename}.vcf" "~{msa_fasta}" @@ -1219,8 +1217,8 @@ task augur_mask_sites { File? mask_bed String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 } - Int disk_size = 100 parameter_meta { sequences: { description: "Set of alignments (fasta format) or variants (vcf format) to mask.", @@ -1275,10 +1273,11 @@ task draft_augur_tree { File? vcf_reference String? tree_builder_args - Int? cpus + Int cpus = 64 + Int machine_mem_gb = 32 String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 1250 } - Int disk_size = 750 parameter_meta { msa_or_vcf: { description: "Set of alignments (fasta format) or variants (vcf format) to construct a tree from using augur tree (iqTree).", @@ -1303,8 +1302,8 @@ task draft_augur_tree { >>> runtime { docker: docker - memory: "32 GB" - cpu: select_first([cpus, 64]) + memory: machine_mem_gb + " GB" + cpu: cpus disks: "local-disk " + disk_size + " LOCAL" disk: disk_size + " GB" # TES dx_instance_type: "mem1_ssd1_v2_x36" @@ -1346,8 +1345,9 @@ task refine_augur_tree { File? vcf_reference String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 + Int machine_mem_gb = 75 } - Int disk_size = 100 parameter_meta { msa_or_vcf: { description: "Set of alignments (fasta format) or variants (vcf format) to use to guide Treetime.", @@ -1386,7 +1386,7 @@ task refine_augur_tree { >>> runtime { docker: docker - memory: "50 GB" + memory: machine_mem_gb + " GB" cpu : 2 disks: "local-disk " + disk_size + " HDD" disk: disk_size + " GB" # TES @@ -1417,11 +1417,11 @@ task ancestral_traits { File? weights Float? sampling_bias_correction - Int? machine_mem_gb + Int machine_mem_gb = 32 String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 } String out_basename = basename(tree, '.nwk') - Int disk_size = 100 command <<< set -e augur version > VERSION @@ -1439,7 +1439,7 @@ task ancestral_traits { >>> runtime { docker: docker - memory: select_first([machine_mem_gb, 32]) + " GB" + memory: machine_mem_gb + " GB" cpu : 4 disks: "local-disk " + disk_size + " HDD" disk: disk_size + " GB" # TES @@ -1472,8 +1472,8 @@ task ancestral_tree { File? output_vcf String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 300 } - Int disk_size = 50 parameter_meta { msa_or_vcf: { description: "Set of alignments (fasta format) or variants (vcf format) to use to guide Treetime.", @@ -1533,9 +1533,9 @@ task translate_augur_tree { File? vcf_reference String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 300 } String out_basename = basename(tree, '.nwk') - Int disk_size = 50 command <<< set -e augur version > VERSION @@ -1588,11 +1588,11 @@ task tip_frequencies { Boolean censored = false Boolean include_internal_nodes = false - Int? machine_mem_gb + Int machine_mem_gb = 64 String docker = "nextstrain/base:build-20211012T204409Z" String out_basename = basename(tree, '.nwk') + Int disk_size = 200 } - Int disk_size = 100 command <<< set -e augur version > VERSION @@ -1621,7 +1621,7 @@ task tip_frequencies { >>> runtime { docker: docker - memory: select_first([machine_mem_gb, 30]) + " GB" + memory: machine_mem_gb + " GB" cpu : 4 disks: "local-disk " + disk_size + " HDD" disk: disk_size + " GB" # TES @@ -1650,9 +1650,9 @@ task assign_clades_to_nodes { File clades_tsv String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 300 } String out_basename = basename(basename(tree_nwk, ".nwk"), "_timetree") - Int disk_size = 50 command <<< set -e augur version > VERSION @@ -1693,11 +1693,11 @@ task augur_import_beast { String? tip_date_format String? tip_date_delimiter - Int? machine_mem_gb + Int machine_mem_gb = 3 String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 150 } String tree_basename = basename(beast_mcc_tree, ".tree") - Int disk_size = 50 command <<< set -e augur version > VERSION @@ -1715,7 +1715,7 @@ task augur_import_beast { >>> runtime { docker: docker - memory: select_first([machine_mem_gb, 3]) + " GB" + memory: machine_mem_gb + " GB" cpu : 2 disks: "local-disk " + disk_size + " HDD" disk: disk_size + " GB" # TES @@ -1754,11 +1754,10 @@ task export_auspice_json { String out_basename = basename(basename(tree, ".nwk"), "_timetree") - Int? machine_mem_gb + Int machine_mem_gb = 64 String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 300 } - - Int disk_size = 100 command <<< set -e -o pipefail @@ -1819,7 +1818,7 @@ task export_auspice_json { >>> runtime { docker: docker - memory: select_first([machine_mem_gb, 64]) + " GB" + memory: machine_mem_gb + " GB" cpu : 4 disks: "local-disk " + disk_size + " HDD" disk: disk_size + " GB" # TES diff --git a/pipes/WDL/tasks/tasks_utils.wdl b/pipes/WDL/tasks/tasks_utils.wdl index f0c5f07e0..bdbc74eb7 100644 --- a/pipes/WDL/tasks/tasks_utils.wdl +++ b/pipes/WDL/tasks/tasks_utils.wdl @@ -721,8 +721,8 @@ task filter_sequences_by_length { Int min_non_N = 1 String docker = "quay.io/broadinstitute/viral-core:2.1.33" + Int disk_size = 750 } - Int disk_size = 300 parameter_meta { sequences_fasta: { description: "Set of sequences in fasta format",