From ea7b24e9a5b4f94021ecb202753fe3681d726af4 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Thu, 16 Jun 2022 11:20:12 -0400 Subject: [PATCH] in export_auspice_json parameterize task mem, raise default to 64GB; increase AUGUR_RECURSION_LIMIT from 10k to 15k --- pipes/WDL/tasks/tasks_nextstrain.wdl | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl index d61f9f842..1344b8e4c 100644 --- a/pipes/WDL/tasks/tasks_nextstrain.wdl +++ b/pipes/WDL/tasks/tasks_nextstrain.wdl @@ -1688,6 +1688,7 @@ task export_auspice_json { String out_basename = basename(basename(tree, ".nwk"), "_timetree") + Int? machine_mem_gb String docker = "nextstrain/base:build-20211012T204409Z" } @@ -1735,7 +1736,7 @@ task export_auspice_json { echo --auspice-config >> exportargs echo "~{auspice_config}" >> exportargs - (export AUGUR_RECURSION_LIMIT=10000; cat exportargs | grep . | tr '\n' '\0' | xargs -0 -t augur export v2 \ + (export AUGUR_RECURSION_LIMIT=15000; cat exportargs | grep . | tr '\n' '\0' | xargs -0 -t augur export v2 \ ~{"--metadata " + sample_metadata} \ ~{"--lat-longs " + lat_longs_tsv} \ ~{"--colors " + colors_tsv} \ @@ -1750,10 +1751,10 @@ task export_auspice_json { >>> runtime { docker: docker - memory: "32 GB" + memory: select_first([machine_mem_gb, 64]) + " GB" cpu : 4 disks: "local-disk 100 HDD" - dx_instance_type: "mem3_ssd1_v2_x4" + dx_instance_type: "mem3_ssd1_v2_x8" preemptible: 0 maxRetries: 2 }