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Remove redundant GetPed task in GatherBatchEvidence.CNMOPS #591

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merged 1 commit into from
Aug 28, 2023
Merged

Remove redundant GetPed task in GatherBatchEvidence.CNMOPS #591

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45 changes: 1 addition & 44 deletions wdl/CNMOPS.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -120,19 +120,11 @@ workflow CNMOPS {
runtime_attr_override = runtime_attr_sample3
}

call GetPed {
input:
ped = ped_file,
samples = samples,
linux_docker = linux_docker,
runtime_attr_override = runtime_attr_ped
}

call CleanCNMops {
input:
chrom_file=chrom_file,
allo_file=allo_file,
samplelist = GetPed.batchped,
samplelist = ped_file,
exclude = exclude_list,
batch = batch,
NR1 = NormalR1.Gff,
Expand All @@ -156,41 +148,6 @@ workflow CNMOPS {
}
}

task GetPed {
input {
File ped
Array[String] samples
String linux_docker
RuntimeAttr? runtime_attr_override
}

RuntimeAttr default_attr = object {
cpu_cores: 1,
mem_gb: 3.75,
disk_gb: 10,
boot_disk_gb: 10,
preemptible_tries: 3,
max_retries: 1
}
RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])

output {
File batchped = "batch.ped"
}
command <<<
egrep '~{sep="|" samples}' ~{ped} > batch.ped
>>>
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"
bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
docker: linux_docker
preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
}
}

task CleanCNMops {
input {
File samplelist
Expand Down