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Add WDL script for normalizing VCF files by removing HAPCOMP and HAPDOM fields" #470

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Add WDL script for normalizing VCF files by removing HAPCOMP and HAPDOM fields" #470

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Add WDL script for normalizing VCF files by removing HAPCOMP and HAPD…
shadizaheri Sep 15, 2024
5955ce5
Disk SSD
shadizaheri Sep 15, 2024
9a4627e
sample id
shadizaheri Sep 15, 2024
af3c2ca
output indexed files
shadizaheri Sep 15, 2024
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add .tbi
shadizaheri Sep 15, 2024
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output indexed files
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@shadizaheri
shadizaheri committed Sep 15, 2024
commit af3c2cad53fd92f58c983e96aec45b382c90a703
18 changes: 12 additions & 6 deletions wdl/malaria/NormalizeVCF.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,10 @@ workflow NormalizeVCF {
input {
File input_vcf
File reference_fa
String sample_name # New input for sample name
Int disk_size_gb = 20
Int memory_gb = 4
Int cpu_cores = 1
String sample_name
Int disk_size_gb = 30
Int memory_gb = 8
Int cpu_cores = 4
}

call RemoveHAPCOMP {
Expand Down Expand Up @@ -38,6 +38,7 @@ workflow NormalizeVCF {

output {
File normalized_vcf = NormalizeVCFFile.output_vcf
File normalized_vcf_index = NormalizeVCFFile.output_vcf_index
}
}

Expand All @@ -61,7 +62,7 @@ task RemoveHAPCOMP {
docker: "us.gcr.io/broad-dsp-lrma/bcftools_htslib:v9152024"
memory: "~{memory_gb}G"
cpu: "~{cpu_cores}"
disks: "local-disk ~{disk_size_gb} HDD"
disks: "local-disk ~{disk_size_gb} SSD"
}
}

Expand All @@ -85,7 +86,7 @@ task RemoveHAPDOM {
docker: "us.gcr.io/broad-dsp-lrma/bcftools_htslib:v9152024"
memory: "~{memory_gb}G"
cpu: "~{cpu_cores}"
disks: "local-disk ~{disk_size_gb} HDD"
disks: "local-disk ~{disk_size_gb} SSD"
}
}

Expand All @@ -100,11 +101,16 @@ task NormalizeVCFFile {
}

command {
# Normalize the VCF
bcftools norm -m -any --atom-overlaps . -f ~{reference_fa} ~{input_vcf} | bgzip -c > ~{sample_name}.norm.vcf.gz

# Index the normalized VCF
bcftools index ~{sample_name}.norm.vcf.gz
}

output {
File output_vcf = "~{sample_name}.norm.vcf.gz"
File output_vcf_index = "~{sample_name}.norm.vcf.gz.csi"
}

runtime {
Expand Down
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