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SV_Pipeline_Full.wdl
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SV_Pipeline_Full.wdl
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version 1.0
import "Pre_Merge_SV.wdl" as premerge
import "Merge_SV.wdl" as merge
import "Post_Merge_SV.wdl" as postmerge
workflow SV_Pipeline_Full {
input {
Array[File] aligned_crams
String aligned_cram_suffix
File ref_fasta
File ref_fasta_index
File ref_cache
File? call_regions_bed
File? call_regions_bed_index
File exclude_regions
File mei_annotation_bed
String cohort
String center
String final_vcf_name
Int preemptible_tries
}
call premerge.Pre_Merge_SV {
input:
aligned_crams = aligned_crams,
aligned_cram_suffix = aligned_cram_suffix,
ref_fasta = ref_fasta,
ref_fasta_index = ref_fasta_index,
ref_cache = ref_cache,
call_regions_bed = call_regions_bed,
call_regions_bed_index = call_regions_bed_index,
exclude_regions = exclude_regions,
cohort = cohort,
center = center,
preemptible_tries = preemptible_tries
}
call merge.Merge_SV {
input:
manta_input_vcfs = Pre_Merge_SV.manta_vcfs,
smoove_input_vcfs = Pre_Merge_SV.smoove_vcfs,
cohort_name = cohort,
preemptible_tries = preemptible_tries
}
call postmerge.Post_Merge_SV {
input:
aligned_crams = aligned_crams,
aligned_cram_indices = Pre_Merge_SV.cram_indices,
cn_hist_roots = Pre_Merge_SV.cnvnator_cn_hist_roots,
manta_vcfs = Pre_Merge_SV.manta_original_vcfs,
aligned_cram_suffix = aligned_cram_suffix,
merged_vcf = Merge_SV.output_vcf,
cohort_name = cohort,
final_vcf_name = final_vcf_name,
ref_fasta = ref_fasta,
ref_fasta_index = ref_fasta_index,
ref_cache = ref_cache,
mei_annotation_bed = mei_annotation_bed,
preemptible_tries = preemptible_tries
}
output {
File output_ped = Post_Merge_SV.output_ped
File output_vcf_bnd = Post_Merge_SV.output_vcf_bnd
File output_vcf_index_bnd = Post_Merge_SV.output_vcf_index_bnd
File output_vcf_del = Post_Merge_SV.output_vcf_del
File output_vcf_ins = Post_Merge_SV.output_vcf_ins
File output_vcf_index_other = Post_Merge_SV.output_vcf_index_other
File output_vcf_other = Post_Merge_SV.output_vcf_other
File output_vcf_index_del = Post_Merge_SV.output_vcf_index_del
File output_vcf_index_ins = Post_Merge_SV.output_vcf_index_ins
}
}