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Compare inferred to reported sex for QC #199

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Merged
williamrowell merged 1 commit into from
Mar 25, 2025
Merged

Compare inferred to reported sex for QC #199

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3 changes: 3 additions & 0 deletions workflows/family.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -385,6 +385,9 @@ workflow humanwgs_family {
File? tertiary_sv_filtered_vcf_index = tertiary_analysis.sv_filtered_vcf_index
File? tertiary_sv_filtered_tsv = tertiary_analysis.sv_filtered_tsv

# qc messages
Array[String?] qc_messages = flatten([upstream.msg_qc_sex])

# workflow metadata
String workflow_name = "humanwgs_family"
String workflow_version = "v3.0.0-alpha1" + if defined(debug_version) then "~{"-" + debug_version}" else ""
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3 changes: 3 additions & 0 deletions workflows/singleton.wdl
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Expand Up @@ -319,6 +319,9 @@ workflow humanwgs_singleton {
File? tertiary_sv_filtered_vcf_index = tertiary_analysis.sv_filtered_vcf_index
File? tertiary_sv_filtered_tsv = tertiary_analysis.sv_filtered_tsv

# qc messages
Array[String?] qc_messages = [upstream.msg_qc_sex]

# workflow metadata
String workflow_name = "humanwgs_family"
String workflow_version = "v3.0.0-alpha1" + if defined(debug_version) then "~{"-" + debug_version}" else ""
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13 changes: 10 additions & 3 deletions workflows/upstream/upstream.wdl
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Expand Up @@ -100,6 +100,10 @@ workflow upstream {
runtime_attributes = default_runtime_attributes
}

if (defined(sex) && (mosdepth.inferred_sex != sex)) {
String qc_sex = "~{sample_id}: Reported sex ~{sex} does not match inferred sex ~{mosdepth.inferred_sex}."
}

call DeepVariant.deepvariant {
input:
sample_id = sample_id,
Expand All @@ -114,7 +118,7 @@ workflow upstream {

call Sawfish.sawfish_discover {
input:
sex = select_first([sex, mosdepth.inferred_sex]),
sex = mosdepth.inferred_sex,
aligned_bam = aligned_bam_data,
aligned_bam_index = aligned_bam_index,
ref_fasta = ref_map["fasta"], # !FileCoercion
Expand All @@ -128,7 +132,7 @@ workflow upstream {
call Trgt.trgt {
input:
sample_id = sample_id,
sex = select_first([sex, mosdepth.inferred_sex]),
sex = mosdepth.inferred_sex,
aligned_bam = aligned_bam_data,
aligned_bam_index = aligned_bam_index,
ref_fasta = ref_map["fasta"], # !FileCoercion
Expand All @@ -151,7 +155,7 @@ workflow upstream {
call Hificnv.hificnv {
input:
sample_id = sample_id,
sex = select_first([sex, mosdepth.inferred_sex]),
sex = mosdepth.inferred_sex,
aligned_bam = aligned_bam_data,
aligned_bam_index = aligned_bam_index,
vcf = deepvariant.vcf,
Expand Down Expand Up @@ -239,5 +243,8 @@ workflow upstream {
String stat_cnv_DEL_count = hificnv.stat_DEL_count
String stat_cnv_DUP_sum = hificnv.stat_DUP_sum
String stat_cnv_DEL_sum = hificnv.stat_DEL_sum

# qc messages
String? msg_qc_sex = qc_sex
}
}