From 403c8c004e692f50fb222dcc60927269b7401fdd Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Wed, 22 Feb 2023 18:43:27 -0500 Subject: [PATCH 01/17] bump disk sizes in nextstrain --- pipes/WDL/tasks/tasks_nextstrain.wdl | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index d077421ce..a01d2cda3 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -102,7 +102,7 @@ task nextclade_many_samples { File? genome_ids_setdefault_blank String docker = "nextstrain/nextclade:2.9.1" } - Int disk_size = 100 + Int disk_size = 150 command <<< set -e apt-get update @@ -633,9 +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: { @@ -690,7 +690,7 @@ task nextstrain_ncov_sanitize_gisaid_data { String docker = "nextstrain/base:build-20211012T204409Z" } - Int disk_size = 375 + Int disk_size = 750 parameter_meta { sequences_gisaid_fasta: { @@ -766,7 +766,7 @@ task filter_subsample_sequences { String docker = "nextstrain/base:build-20211012T204409Z" } - Int disk_size = 100 + Int disk_size = 750 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.", @@ -851,7 +851,7 @@ 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 = 200 + Int disk_size = 750 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.", @@ -1189,7 +1189,7 @@ task snp_sites { String docker = "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0" } String out_basename = basename(msa_fasta, ".fasta") - Int disk_size = 100 + Int disk_size = 375 command { snp-sites -V > VERSION snp-sites -v ~{true="" false="-c" allow_wildcard_bases} -o "~{out_basename}.vcf" "~{msa_fasta}" @@ -1220,7 +1220,7 @@ task augur_mask_sites { String docker = "nextstrain/base:build-20211012T204409Z" } - Int disk_size = 100 + Int disk_size = 375 parameter_meta { sequences: { description: "Set of alignments (fasta format) or variants (vcf format) to mask.", @@ -1347,7 +1347,7 @@ task refine_augur_tree { String docker = "nextstrain/base:build-20211012T204409Z" } - Int disk_size = 100 + Int disk_size = 375 parameter_meta { msa_or_vcf: { description: "Set of alignments (fasta format) or variants (vcf format) to use to guide Treetime.", @@ -1421,7 +1421,7 @@ task ancestral_traits { String docker = "nextstrain/base:build-20211012T204409Z" } String out_basename = basename(tree, '.nwk') - Int disk_size = 100 + Int disk_size = 375 command <<< set -e augur version > VERSION @@ -1473,7 +1473,7 @@ task ancestral_tree { String docker = "nextstrain/base:build-20211012T204409Z" } - Int disk_size = 50 + Int disk_size = 150 parameter_meta { msa_or_vcf: { description: "Set of alignments (fasta format) or variants (vcf format) to use to guide Treetime.", @@ -1535,7 +1535,7 @@ task translate_augur_tree { String docker = "nextstrain/base:build-20211012T204409Z" } String out_basename = basename(tree, '.nwk') - Int disk_size = 50 + Int disk_size = 150 command <<< set -e augur version > VERSION @@ -1652,7 +1652,7 @@ task assign_clades_to_nodes { String docker = "nextstrain/base:build-20211012T204409Z" } String out_basename = basename(basename(tree_nwk, ".nwk"), "_timetree") - Int disk_size = 50 + Int disk_size = 150 command <<< set -e augur version > VERSION @@ -1697,7 +1697,7 @@ task augur_import_beast { String docker = "nextstrain/base:build-20211012T204409Z" } String tree_basename = basename(beast_mcc_tree, ".tree") - Int disk_size = 50 + Int disk_size = 150 command <<< set -e augur version > VERSION @@ -1758,7 +1758,7 @@ task export_auspice_json { String docker = "nextstrain/base:build-20211012T204409Z" } - Int disk_size = 100 + Int disk_size = 150 command <<< set -e -o pipefail From f626c5e783f1215bd1884a439b92add02fbc5830 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 28 Feb 2023 08:27:54 -0500 Subject: [PATCH 02/17] parameterize more disk_size specs in nextstrain related tasks --- pipes/WDL/tasks/tasks_nextstrain.wdl | 57 +++++++++++++--------------- pipes/WDL/tasks/tasks_utils.wdl | 2 +- 2 files changed, 28 insertions(+), 31 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index a01d2cda3..73f5936cf 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -14,9 +14,9 @@ task nextclade_one_sample { File? virus_properties String? dataset_name String docker = "nextstrain/nextclade:2.9.1" + Int disk_size = 50 } String basename = basename(genome_fasta, ".fasta") - Int disk_size = 50 command { set -e apt-get update @@ -101,8 +101,8 @@ task nextclade_many_samples { String basename File? genome_ids_setdefault_blank String docker = "nextstrain/nextclade:2.9.1" + Int disk_size = 150 } - Int disk_size = 150 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." @@ -394,9 +394,9 @@ task filter_segments { 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 = 375 } 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" @@ -636,7 +636,6 @@ task nextstrain_deduplicate_sequences { Int disk_size = 750 } - 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 = 750 - 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 = 750 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 = 750 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 @@ -1040,8 +1038,8 @@ task mafft_one_chr_chunked { String docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2" Int mem_size = 32 Int cpus = 96 + 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 = 375 } String out_basename = basename(msa_fasta, ".fasta") - Int disk_size = 375 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 = 375 } - Int disk_size = 375 parameter_meta { sequences: { description: "Set of alignments (fasta format) or variants (vcf format) to mask.", @@ -1277,8 +1275,8 @@ task draft_augur_tree { Int? cpus String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 750 } - 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).", @@ -1346,8 +1344,8 @@ task refine_augur_tree { File? vcf_reference String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 375 } - Int disk_size = 375 parameter_meta { msa_or_vcf: { description: "Set of alignments (fasta format) or variants (vcf format) to use to guide Treetime.", @@ -1419,9 +1417,9 @@ task ancestral_traits { Int? machine_mem_gb String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 375 } String out_basename = basename(tree, '.nwk') - Int disk_size = 375 command <<< set -e augur version > VERSION @@ -1472,8 +1470,8 @@ task ancestral_tree { File? output_vcf String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 150 } - Int disk_size = 150 parameter_meta { msa_or_vcf: { description: "Set of alignments (fasta format) or variants (vcf format) to use to guide Treetime.", @@ -1533,9 +1531,9 @@ task translate_augur_tree { File? vcf_reference String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 150 } String out_basename = basename(tree, '.nwk') - Int disk_size = 150 command <<< set -e augur version > VERSION @@ -1591,8 +1589,8 @@ task tip_frequencies { Int? machine_mem_gb String docker = "nextstrain/base:build-20211012T204409Z" String out_basename = basename(tree, '.nwk') + Int disk_size = 100 } - Int disk_size = 100 command <<< set -e augur version > VERSION @@ -1650,9 +1648,9 @@ task assign_clades_to_nodes { File clades_tsv String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 150 } String out_basename = basename(basename(tree_nwk, ".nwk"), "_timetree") - Int disk_size = 150 command <<< set -e augur version > VERSION @@ -1695,9 +1693,9 @@ task augur_import_beast { Int? machine_mem_gb String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 150 } String tree_basename = basename(beast_mcc_tree, ".tree") - Int disk_size = 150 command <<< set -e augur version > VERSION @@ -1756,9 +1754,8 @@ task export_auspice_json { Int? machine_mem_gb String docker = "nextstrain/base:build-20211012T204409Z" + Int disk_size = 150 } - - Int disk_size = 150 command <<< set -e -o pipefail 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", From d6906d17b637ad3c48379bca58573c723f55dcf5 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 28 Feb 2023 21:32:38 -0500 Subject: [PATCH 03/17] reduce cpu request --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 73f5936cf..d99c2bec8 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1037,7 +1037,7 @@ 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 } command <<< From 13f64b1f8610649d434ff75eb477efb9876cf015 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Fri, 3 Mar 2023 08:06:34 -0500 Subject: [PATCH 04/17] parameterize and increase default ram for refine augur tree --- pipes/WDL/tasks/tasks_nextstrain.wdl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 73f5936cf..8721ba3c0 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1345,6 +1345,7 @@ task refine_augur_tree { String docker = "nextstrain/base:build-20211012T204409Z" Int disk_size = 375 + Int machine_mem_gb = 75 } parameter_meta { msa_or_vcf: { @@ -1384,7 +1385,7 @@ 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 From bc7ba01e5dc801c319c52968b4b6fd9c2ae5e5b6 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 7 Mar 2023 10:52:30 -0500 Subject: [PATCH 05/17] change more vm parameterization from select_first to actual default input values --- pipes/WDL/tasks/tasks_nextstrain.wdl | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index dd972667e..54eac97e4 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1273,7 +1273,8 @@ 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 = 750 } @@ -1301,8 +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" @@ -1416,7 +1417,7 @@ 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 = 375 } @@ -1438,7 +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 @@ -1587,7 +1588,7 @@ task tip_frequencies { Boolean censored = false Boolean include_internal_nodes = false - Int? machine_mem_gb + Int machine_mem_gb = 50 String docker = "nextstrain/base:build-20211012T204409Z" String out_basename = basename(tree, '.nwk') Int disk_size = 100 @@ -1620,7 +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 @@ -1692,7 +1693,7 @@ 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 } @@ -1714,7 +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 @@ -1753,7 +1754,7 @@ 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 = 150 } @@ -1817,7 +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 From ed106c0cf164fa872086094511eb700239aae6b2 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 7 Mar 2023 11:06:35 -0500 Subject: [PATCH 06/17] bump to latest observed usage --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 54eac97e4..cc887c9d1 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1588,7 +1588,7 @@ task tip_frequencies { Boolean censored = false Boolean include_internal_nodes = false - Int machine_mem_gb = 50 + Int machine_mem_gb = 64 String docker = "nextstrain/base:build-20211012T204409Z" String out_basename = basename(tree, '.nwk') Int disk_size = 100 From 11c78853765efba334adc6e9f52eb156e38daba2 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:42:51 -0500 Subject: [PATCH 07/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index cc887c9d1..cde7e59fd 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -452,7 +452,7 @@ task nextstrain_build_subsample { Int machine_mem_gb = 50 String docker = "nextstrain/base:build-20211012T204409Z" String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a" - Int disk_size = 375 + Int disk_size = 750 } parameter_meta { alignment_msa_fasta: { From f984aa36022a131ab2e53b1ced20a32a8b3d9081 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:43:26 -0500 Subject: [PATCH 08/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index cde7e59fd..5b8c32ec5 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1185,7 +1185,7 @@ 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 = 375 + Int disk_size = 750 } String out_basename = basename(msa_fasta, ".fasta") command { From 9a2e64b856006a011cddedf23ca1dcd70e80aee2 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:43:35 -0500 Subject: [PATCH 09/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 5b8c32ec5..e19b8ade1 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1217,7 +1217,7 @@ task augur_mask_sites { File? mask_bed String docker = "nextstrain/base:build-20211012T204409Z" - Int disk_size = 375 + Int disk_size = 750 } parameter_meta { sequences: { From 8e2a5d7f368879e9f858954691d2358f73a51f63 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:43:46 -0500 Subject: [PATCH 10/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index e19b8ade1..654c29e24 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1276,7 +1276,7 @@ task draft_augur_tree { Int cpus = 64 Int machine_mem_gb = 32 String docker = "nextstrain/base:build-20211012T204409Z" - Int disk_size = 750 + Int disk_size = 1250 } parameter_meta { msa_or_vcf: { From 185131dc7b333e94f1c693cc87acb64e974d8b95 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:43:56 -0500 Subject: [PATCH 11/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 654c29e24..0091cc348 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1345,7 +1345,7 @@ task refine_augur_tree { File? vcf_reference String docker = "nextstrain/base:build-20211012T204409Z" - Int disk_size = 375 + Int disk_size = 750 Int machine_mem_gb = 75 } parameter_meta { From 485f50b599c1374609fd9f718bf7cc373b99986b Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:44:12 -0500 Subject: [PATCH 12/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 0091cc348..7be0a360f 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1591,7 +1591,7 @@ task tip_frequencies { Int machine_mem_gb = 64 String docker = "nextstrain/base:build-20211012T204409Z" String out_basename = basename(tree, '.nwk') - Int disk_size = 100 + Int disk_size = 200 } command <<< set -e From 6e7e969878160d22ec01f4417f35186deb489c0b Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:44:25 -0500 Subject: [PATCH 13/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 7be0a360f..dd472e78d 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1472,7 +1472,7 @@ task ancestral_tree { File? output_vcf String docker = "nextstrain/base:build-20211012T204409Z" - Int disk_size = 150 + Int disk_size = 300 } parameter_meta { msa_or_vcf: { From b37553ceba0e60d5d4378f0f87a33ef9b6dea85a Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:44:37 -0500 Subject: [PATCH 14/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index dd472e78d..6ab51b35c 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1533,7 +1533,7 @@ task translate_augur_tree { File? vcf_reference String docker = "nextstrain/base:build-20211012T204409Z" - Int disk_size = 150 + Int disk_size = 300 } String out_basename = basename(tree, '.nwk') command <<< From 2f0745e3b2808c341bfa96f687fe3beb51bcb347 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:44:46 -0500 Subject: [PATCH 15/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 6ab51b35c..9c8cbeb88 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1756,7 +1756,7 @@ task export_auspice_json { Int machine_mem_gb = 64 String docker = "nextstrain/base:build-20211012T204409Z" - Int disk_size = 150 + Int disk_size = 300 } command <<< From 79b571d4838b9c116f387b2af2c38451085b9c7f Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:44:52 -0500 Subject: [PATCH 16/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index 9c8cbeb88..df75a82cb 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1650,7 +1650,7 @@ task assign_clades_to_nodes { File clades_tsv String docker = "nextstrain/base:build-20211012T204409Z" - Int disk_size = 150 + Int disk_size = 300 } String out_basename = basename(basename(tree_nwk, ".nwk"), "_timetree") command <<< From 3048552d5ce5e4992fb71608c4edab1614b640e1 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Tue, 7 Mar 2023 14:45:24 -0500 Subject: [PATCH 17/17] double default VM disk shapes Co-authored-by: Christian Freitas --- pipes/WDL/tasks/tasks_nextstrain.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index df75a82cb..8fb09ecd8 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1419,7 +1419,7 @@ task ancestral_traits { Int machine_mem_gb = 32 String docker = "nextstrain/base:build-20211012T204409Z" - Int disk_size = 375 + Int disk_size = 750 } String out_basename = basename(tree, '.nwk') command <<<