Skip to content

Commit

Permalink
Made zarr conversion optional in SRJointCallGVCFsWithGenomicsDB.wdl (#…
Browse files Browse the repository at this point in the history
  • Loading branch information
jonn-smith authored Dec 18, 2024
1 parent c304367 commit 0ab9499
Showing 1 changed file with 12 additions and 7 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,7 @@ workflow SRJointCallGVCFsWithGenomicsDB {
File? interval_list

Boolean use_gnarly_genotyper = false
Boolean do_zarr_conversion = false

Int shard_max_interval_size_bp = 999999999

Expand Down Expand Up @@ -387,12 +388,14 @@ workflow SRJointCallGVCFsWithGenomicsDB {
prefix = prefix + ".rescored.combined"
}

# Convert to Zarr
call SGKit.ConvertToZarrStore as ConvertToZarr {
input:
vcf = GatherRescoredVcfs.output_vcf,
tbi = GatherRescoredVcfs.output_vcf_index,
prefix = prefix
if (do_zarr_conversion) {
# Convert to Zarr
call SGKit.ConvertToZarrStore as ConvertToZarr {
input:
vcf = GatherRescoredVcfs.output_vcf,
tbi = GatherRescoredVcfs.output_vcf_index,
prefix = prefix
}
}

# Convert the output to a HAIL Matrix Table:
Expand Down Expand Up @@ -500,7 +503,9 @@ workflow SRJointCallGVCFsWithGenomicsDB {
}
}

call FF.FinalizeToFile as FinalizeZarr { input: outdir = outdir, keyfile = keyfile, file = ConvertToZarr.zarr }
if (do_zarr_conversion) {
call FF.FinalizeToFile as FinalizeZarr { input: outdir = outdir, keyfile = keyfile, file = select_first([ConvertToZarr.zarr]) }
}

call FF.FinalizeToFile as FinalizeHailMatrixTable {
input:
Expand Down

0 comments on commit 0ab9499

Please sign in to comment.