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Add subset ped step at start of CleanVcf #250

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merged 1 commit into from
Dec 21, 2021
Merged

Add subset ped step at start of CleanVcf #250

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20 changes: 19 additions & 1 deletion wdl/CleanVcf.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ version 1.0

import "CleanVcfChromosome.wdl" as CleanVcfChromosome
import "TasksMakeCohortVcf.wdl" as MiniTasks
import "Utils.wdl" as util

workflow CleanVcf {
input {
Expand Down Expand Up @@ -43,6 +44,23 @@ workflow CleanVcf {
RuntimeAttr? runtime_override_combine_clean_vcf_2
RuntimeAttr? runtime_override_combine_revised_4
RuntimeAttr? runtime_override_combine_multi_ids_4
RuntimeAttr? runtime_attr_ids_from_vcf
RuntimeAttr? runtime_attr_subset_ped
}

call util.GetSampleIdsFromVcf {
input:
vcf = complex_genotype_vcfs[0],
sv_base_mini_docker = sv_base_mini_docker,
runtime_attr_override = runtime_attr_ids_from_vcf
}
call util.SubsetPedFile {
input:
ped_file = merged_ped_file,
sample_list = GetSampleIdsFromVcf.out_file,
subset_name = "vcf_samples",
sv_base_mini_docker = sv_base_mini_docker,
runtime_attr_override = runtime_attr_subset_ped
}

#Scatter per chromosome
Expand All @@ -55,7 +73,7 @@ workflow CleanVcf {
vcf=complex_genotype_vcfs[i],
contig=contig,
background_list=complex_resolve_background_fail_lists[i],
ped_file=merged_ped_file,
ped_file=SubsetPedFile.ped_subset_file,
bothsides_pass_list=complex_resolve_bothside_pass_lists[i],
allosome_fai=allosome_fai,
prefix=cohort_name,
Expand Down
4 changes: 3 additions & 1 deletion wdl/MakeCohortVcf.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -328,7 +328,9 @@ workflow MakeCohortVcf {
runtime_override_split_include_list=runtime_override_split_include_list,
runtime_override_combine_clean_vcf_2=runtime_override_combine_clean_vcf_2,
runtime_override_combine_revised_4=runtime_override_combine_revised_4,
runtime_override_combine_multi_ids_4=runtime_override_combine_multi_ids_4
runtime_override_combine_multi_ids_4=runtime_override_combine_multi_ids_4,
runtime_attr_ids_from_vcf=runtime_attr_ids_from_vcf,
runtime_attr_subset_ped=runtime_attr_subset_ped
}

Array[String] contigs = transpose(read_tsv(contig_list))[0]
Expand Down