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Localize CRAM in the Whamg workflow instead of leveraging streaming from GCS directly #550

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Localize CRAM in the Whamg workflow instead of leveraging streaming from GCS directly #550

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7b112a0
Localize files instead of streaming, for CoA compatibility.
VJalili Jun 15, 2023
da698c7
Determine cromwell root using a more portable approach.
VJalili Sep 15, 2023
1b73c16
Localize files instead of streaming, for CoA compatibility.
VJalili Nov 22, 2023
60f0b9e
Localize files instead of streaming, for CoA compatibility.
VJalili Nov 22, 2023
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2 changes: 1 addition & 1 deletion wdl/GATKSVPipelineBatch.wdl
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Expand Up @@ -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

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6 changes: 4 additions & 2 deletions wdl/GatherSampleEvidence.wdl
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Expand Up @@ -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)
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4 changes: 2 additions & 2 deletions wdl/MELT.wdl
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Expand Up @@ -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)
Expand Down Expand Up @@ -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])
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2 changes: 1 addition & 1 deletion wdl/MakeBincovMatrix.wdl
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Expand Up @@ -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
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6 changes: 3 additions & 3 deletions wdl/TestUtils.wdl
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Expand Up @@ -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])
Expand Down Expand Up @@ -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])
Expand Down Expand Up @@ -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])
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12 changes: 0 additions & 12 deletions wdl/Whamg.wdl
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Expand Up @@ -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
Expand Down Expand Up @@ -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

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