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Pre_Merge_SV.wdl
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Pre_Merge_SV.wdl
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version 1.0
import "Pre_Merge_SV_per_sample.wdl" as per_sample
import "Pre_Merge_QC_per_sample.wdl" as qc
import "SV_Tasks.wdl" as SV
workflow Pre_Merge_SV {
input {
Array[File] aligned_crams
String aligned_cram_suffix
# reference inputs
File ref_fasta
File ref_fasta_index
File ref_cache
File? call_regions_bed
File? call_regions_bed_index
File exclude_regions
String cohort
String center
# system inputs
Int preemptible_tries
}
scatter (i in range(length(aligned_crams))) {
File aligned_cram = aligned_crams[i]
call per_sample.Pre_Merge_SV_Per_Sample {
input:
aligned_cram = aligned_cram,
aligned_cram_suffix = aligned_cram_suffix,
ref_fasta = ref_fasta,
ref_fasta_index = ref_fasta_index,
call_regions_bed = call_regions_bed,
call_regions_bed_index = call_regions_bed_index,
ref_cache = ref_cache,
exclude_regions = exclude_regions,
preemptible_tries = preemptible_tries
}
call qc.Pre_Merge_QC_Per_Sample {
input:
manta_vcf = Pre_Merge_SV_Per_Sample.manta_vcf,
lumpy_vcf = Pre_Merge_SV_Per_Sample.smoove_vcf,
cnvnator_vcf = Pre_Merge_SV_Per_Sample.cnvnator_output_cn_txt,
cohort = cohort,
center = center,
preemptible_tries = preemptible_tries
}
}
#scatter (p in [("manta", Pre_Merge_QC_Per_Sample.manta_counts), ("lumpy", Pre_Merge_QC_Per_Sample.lumpy_counts)]) {
# call SV.Make_Count_Plot {
# input:
# name=p.left,
# count_files=p.right
# }
#}
output {
Array[File] cram_indices = Pre_Merge_SV_Per_Sample.cram_index
Array[File] manta_vcfs = Pre_Merge_SV_Per_Sample.manta_vcf
Array[File] manta_tbis = Pre_Merge_SV_Per_Sample.manta_tbi
Array[File] manta_original_vcfs = Pre_Merge_SV_Per_Sample.manta_original_vcf
Array[File] manta_original_tbis = Pre_Merge_SV_Per_Sample.manta_original_tbi
Array[File] cnvnator_cn_hist_roots = Pre_Merge_SV_Per_Sample.cnvnator_cn_hist_root
Array[File] cnvnator_output_cn_txt_files = Pre_Merge_SV_Per_Sample.cnvnator_output_cn_txt
Array[File] cnvnator_cn_bed_files = Pre_Merge_SV_Per_Sample.cnvnator_cn_bed
Array[File] smoove_vcfs = Pre_Merge_SV_Per_Sample.smoove_vcf
Array[File] smoove_csis = Pre_Merge_SV_Per_Sample.smoove_csi
Array[File] lumpy_counts = Pre_Merge_QC_Per_Sample.lumpy_counts
Array[File] manta_counts = Pre_Merge_QC_Per_Sample.manta_counts
#Array[File] count_plots = Make_Count_Plot.counts_plot
}
}