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Allow reblocking TDR/DRS VCFs #1463

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Allow reblocking TDR/DRS VCFs #1463

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bdd2cf0
Allow reblocking TDR/DRS VCFs
kshakir Jan 4, 2025
7db658c
Merge branch 'develop' into ks_reblock_drs
nikellepetrillo Jan 9, 2025
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9 changes: 4 additions & 5 deletions tasks/broad/GermlineVariantDiscovery.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -217,20 +217,19 @@ task Reblock {
}

Int disk_size = ceil((size(gvcf, "GiB")) * 4) + additional_disk
String gvcf_basename = basename(gvcf)
String gvcf_index_basename = basename(gvcf_index)

command {
set -e

# We can't always assume the index was located with the gvcf, so make a link so that the paths look the same
ln -s ~{gvcf} ~{gvcf_basename}
ln -s ~{gvcf_index} ~{gvcf_index_basename}
# Use bash basename instead of WDL to support DRS: https://support.terra.bio/hc/en-us/community/posts/4405396480027
ln -s ~{gvcf} $(basename ~{gvcf})
ln -s ~{gvcf_index} $(basename ~{gvcf_index})

gatk --java-options "-Xms3000m -Xmx3000m" \
ReblockGVCF \
-R ~{ref_fasta} \
-V ~{gvcf_basename} \
-V $(basename ~{gvcf}) \
-do-qual-approx \
--floor-blocks -GQB 20 -GQB 30 -GQB 40 \
~{annotations_to_keep_command} \
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10 changes: 4 additions & 6 deletions tasks/broad/Qc.wdl
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Expand Up @@ -627,9 +627,6 @@ task ValidateVCF {
Int machine_mem_mb = 7000
}

String calling_interval_list_basename = basename(calling_interval_list)
String calling_interval_list_index_basename = if calling_intervals_defined then "" else basename(select_first([calling_interval_list_index]))

Int command_mem_mb = machine_mem_mb - 2000
Float ref_size = size(ref_fasta, "GiB") + size(ref_fasta_index, "GiB") + size(ref_dict, "GiB")
Int disk_size = ceil(size(input_vcf, "GiB") + size(calling_interval_list, "GiB") + size(dbsnp_vcf, "GiB") + ref_size) + 20
Expand All @@ -639,10 +636,11 @@ task ValidateVCF {

if [ ~{calling_intervals_defined} == "false" ]; then
# We can't always assume the index was located with the vcf, so make a link so that the paths look the same
ln -s ~{calling_interval_list} ~{calling_interval_list_basename}
ln -s ~{calling_interval_list_index} ~{calling_interval_list_index_basename}
# Use bash basename instead of WDL to support DRS: https://support.terra.bio/hc/en-us/community/posts/4405396480027
ln -s ~{calling_interval_list} $(basename ~{calling_interval_list})
ln -s ~{calling_interval_list_index} $(basename ~{calling_interval_list_index})
gatk --java-options "-Xms~{command_mem_mb}m -Xmx~{command_mem_mb}m" \
VcfToIntervalList -I ~{calling_interval_list_basename} -O intervals_from_gvcf.interval_list --VARIANT_ID_METHOD USE_FIRST
VcfToIntervalList -I $(basename ~{calling_interval_list}) -O intervals_from_gvcf.interval_list --VARIANT_ID_METHOD USE_FIRST
INTERVALS="intervals_from_gvcf.interval_list"
else
INTERVALS="~{calling_interval_list}"
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