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TSPS-142 updates to help creating simulated reference panel and running imputation against it #1296

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merged 13 commits into from
Jun 10, 2024
Merged

TSPS-142 updates to help creating simulated reference panel and running imputation against it #1296

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9c6bb49
change hardcoded reference base path
Jun 3, 2024
5491d14
change to 6k samples
Jun 4, 2024
d205ccc
change to 3k samples
Jun 4, 2024
c373c68
update liftoverVCFs wdl to have configurable memory
Jun 4, 2024
270652e
set java initial and max heap size
Jun 4, 2024
f727155
try less records in memory
Jun 4, 2024
2e5191f
change reference panel path to 5k sim samples
Jun 4, 2024
5f07c3b
dont need hg38 prefix
Jun 4, 2024
ca15114
add optional error count override for testing
Jun 5, 2024
3d2d479
change reference panel to 10k sim panel
Jun 6, 2024
a21204a
revert lifovervcf changes and change name of reference file basename
Jun 7, 2024
afe3499
spacing
Jun 9, 2024
c49363f
rename reference base prefix variable
Jun 10, 2024
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12 changes: 7 additions & 5 deletions pipelines/broad/arrays/imputation_beagle/ImputationBeaglePreChunk.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ workflow ImputationBeagle {

File ref_dict # for reheadering / adding contig lengths in the header of the ouptut VCF, and calculating contig lengths
Array[String] contigs
String reference_panel_path # path to the bucket where the reference panel files are stored for all contigs
String reference_panel_path_prefix # path + file prefix to the bucket where the reference panel files are stored for all contigs
String genetic_maps_path # path to the bucket where genetic maps are stored for all contigs
String output_basename # the basename for intermediate and output files

Expand All @@ -24,6 +24,8 @@ workflow ImputationBeagle {
String bref3_suffix = ".bref3"

String gatk_docker = "broadinstitute/gatk-nightly:2024-06-06-4.5.0.0-36-g2a420e483-NIGHTLY-SNAPSHOT"

Int? error_count_override
}

call tasks.CountSamples {
Expand All @@ -40,12 +42,12 @@ workflow ImputationBeagle {

scatter (contig_index in range(length(contigs))) {
# these are specific to hg38 - contig is format 'chr1'
String reference_filename = reference_panel_path + "hgdp.tgp.gwaspy.merged." + contigs[contig_index] + ".merged.AN_added.bcf.ac2"
String reference_basename = reference_panel_path_prefix + "." + contigs[contig_index]
String genetic_map_filename = genetic_maps_path + "plink." + contigs[contig_index] + ".GRCh38.withchr.map"

ReferencePanelContig referencePanelContig = {
"interval_list": reference_filename + interval_list_suffix,
"bref3": reference_filename + bref3_suffix,
"interval_list": reference_basename + interval_list_suffix,
"bref3": reference_basename + bref3_suffix,
"contig": contigs[contig_index],
"genetic_map": genetic_map_filename
}
Expand Down Expand Up @@ -107,7 +109,7 @@ workflow ImputationBeagle {

# if any chunk for any chromosome fail CheckChunks, then we will not impute run any task in the next scatter,
# namely phasing and imputing which would be the most costly to throw away
Int n_failed_chunks_int = read_int(StoreContigLevelChunksInfo.n_failed_chunks)
Int n_failed_chunks_int = select_first([error_count_override, read_int(StoreContigLevelChunksInfo.n_failed_chunks)])
call tasks.ErrorWithMessageIfErrorCountNotZero as FailQCNChunks {
input:
errorCount = n_failed_chunks_int,
Expand Down
1 change: 0 additions & 1 deletion pipelines/broad/arrays/imputation_beagle/LiftoverVcfs.wdl
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Expand Up @@ -62,7 +62,6 @@ task LiftOverArrays {
Int disk_size_from_file = (ceil(size(input_vcf, "GiB") + size(liftover_chain, "GiB") + size(reference_fasta, "GiB")) * 2) + 20
Int disk_size = if ( disk_size_from_file > min_disk_size ) then disk_size_from_file else min_disk_size


command <<<
set -euo pipefail

Expand Down