From 7b112a05e55a0f35b79a0ec10ff849fab6facd32 Mon Sep 17 00:00:00 2001 From: VJalili Date: Thu, 15 Jun 2023 15:21:31 -0400 Subject: [PATCH 1/4] Localize files instead of streaming, for CoA compatibility. --- wdl/Whamg.wdl | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/wdl/Whamg.wdl b/wdl/Whamg.wdl index 69942c91f..74c786784 100644 --- a/wdl/Whamg.wdl +++ b/wdl/Whamg.wdl @@ -199,15 +199,6 @@ task RunWhamgOnCram { RuntimeAttr? runtime_attr_override } - parameter_meta { - cram_file: { - localization_optional: true - } - cram_index: { - localization_optional: true - } - } - Array[String] chr_list = read_lines(primary_contigs_list) # Calculate default disk size @@ -250,9 +241,6 @@ task RunWhamgOnCram { df -h echo "whamg $(whamg 2>&1 | grep Version)" - # necessary for getting permission to read from google bucket directly - export GCS_OAUTH_TOKEN=`gcloud auth application-default print-access-token` - # covert cram to bam samtools view -b1@ ~{cpu_cores} -T "~{reference_fasta}" "~{cram_file}" > sample.bam From da698c75b37197ad5f75bc15a5906945abc50add Mon Sep 17 00:00:00 2001 From: VJalili Date: Fri, 15 Sep 2023 08:36:28 -0400 Subject: [PATCH 2/4] Determine cromwell root using a more portable approach. --- wdl/MELT.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl/MELT.wdl b/wdl/MELT.wdl index 83657c7e8..cec90e0d1 100644 --- a/wdl/MELT.wdl +++ b/wdl/MELT.wdl @@ -510,7 +510,7 @@ task RunMELT { # these locations should be stable MELT_DIR="/MELT" - CROMWELL_ROOT="/cromwell_root" + CROMWELL_ROOT="$PWD" # these locations may vary based on MELT version number, so find them: MELT_ROOT=$(find "$MELT_DIR" -name "MELT.jar" | xargs -n1 dirname) From 1b73c162131f48f227f5f68a107a22a85918b93f Mon Sep 17 00:00:00 2001 From: VJalili Date: Wed, 22 Nov 2023 08:58:37 -0500 Subject: [PATCH 3/4] Localize files instead of streaming, for CoA compatibility. --- wdl/GatherSampleEvidence.wdl | 6 ++++-- wdl/MELT.wdl | 2 +- wdl/MakeBincovMatrix.wdl | 2 +- wdl/TestUtils.wdl | 6 +++--- 4 files changed, 9 insertions(+), 7 deletions(-) diff --git a/wdl/GatherSampleEvidence.wdl b/wdl/GatherSampleEvidence.wdl index 09694b27d..4b180ca7a 100644 --- a/wdl/GatherSampleEvidence.wdl +++ b/wdl/GatherSampleEvidence.wdl @@ -328,8 +328,10 @@ task LocalizeReads { Int disk_size = ceil(50 + size(reads_path, "GB")) command { - ln -s ~{reads_path} - ln -s ~{reads_index} + set -exuo pipefail + + mv ~{reads_path} $(basename ~{reads_path}) + mv ~{reads_index} $(basename ~{reads_index}) } output { File output_file = basename(reads_path) diff --git a/wdl/MELT.wdl b/wdl/MELT.wdl index cec90e0d1..b49daaf84 100644 --- a/wdl/MELT.wdl +++ b/wdl/MELT.wdl @@ -542,7 +542,7 @@ task RunMELT { runtime { cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores]) memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" - disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" + disks: "local-disk 100 HDD" #+ select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb]) docker: melt_docker preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries]) diff --git a/wdl/MakeBincovMatrix.wdl b/wdl/MakeBincovMatrix.wdl index d17aa0427..eb18dbc4b 100644 --- a/wdl/MakeBincovMatrix.wdl +++ b/wdl/MakeBincovMatrix.wdl @@ -270,7 +270,7 @@ task ZPaste { runtime { cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores]) - memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" + memory: "4 GiB" # select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB" disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD" bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb]) docker: sv_base_docker diff --git a/wdl/TestUtils.wdl b/wdl/TestUtils.wdl index 407435572..fb4de9a20 100644 --- a/wdl/TestUtils.wdl +++ b/wdl/TestUtils.wdl @@ -125,7 +125,7 @@ task VCFMetrics { >>> runtime { memory: select_first([runtime_override.mem_gb, runtime_default.mem_gb]) + " GB" - disks: "local-disk " + select_first([runtime_override.disk_gb, runtime_default.disk_gb]) + " HDD" + disks: "local-disk 100 HDD" #+ select_first([runtime_override.disk_gb, runtime_default.disk_gb]) + " HDD" cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) @@ -245,7 +245,7 @@ task PEMetrics { >>> runtime { memory: select_first([runtime_override.mem_gb, runtime_default.mem_gb]) + " GB" - disks: "local-disk " + select_first([runtime_override.disk_gb, runtime_default.disk_gb]) + " HDD" + disks: "local-disk 100 HDD" #+ select_first([runtime_override.disk_gb, runtime_default.disk_gb]) + " HDD" cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) @@ -282,7 +282,7 @@ task CountsMetrics { >>> runtime { memory: select_first([runtime_override.mem_gb, runtime_default.mem_gb]) + " GB" - disks: "local-disk " + select_first([runtime_override.disk_gb, runtime_default.disk_gb]) + " HDD" + disks: "local-disk 100 HDD" #+ select_first([runtime_override.disk_gb, runtime_default.disk_gb]) + " HDD" cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores]) preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries]) maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries]) From 60f0b9ec4e90dd9ba1c429c7c2dd90f58c7c1a52 Mon Sep 17 00:00:00 2001 From: VJalili Date: Wed, 22 Nov 2023 09:03:25 -0500 Subject: [PATCH 4/4] Localize files instead of streaming, for CoA compatibility. --- wdl/GATKSVPipelineBatch.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl/GATKSVPipelineBatch.wdl b/wdl/GATKSVPipelineBatch.wdl index 0706f4d79..5cee00990 100644 --- a/wdl/GATKSVPipelineBatch.wdl +++ b/wdl/GATKSVPipelineBatch.wdl @@ -37,7 +37,7 @@ workflow GATKSVPipelineBatch { # Enable different callers Boolean use_manta = true - Boolean use_melt = true + Boolean use_melt = false Boolean use_scramble = true Boolean use_wham = true