Merge branch 'develop' into TSPS-715_glimpse_qc_wdl

Author: mmorgantaylor

.dockstore.yml

@@ -137,6 +137,10 @@ workflows:
     subclass: WDL
     primaryDescriptorPath: /all_of_us/mitochondria/mitochondria_pipeline.wdl
 
+  - name: MitoPostProcessing
+    subclass: WDL
+    primaryDescriptorPath: /all_of_us/mitochondria/MitoPostProcessing.wdl
+  
   - name: mt_coverage_merge
     subclass: WDL
     primaryDescriptorPath: /all_of_us/mitochondria/mt_coverage_merge.wdl

all_of_us/mitochondria/MitoPostProcessing.changelog.md

@@ -0,0 +1,3 @@
+# aou_9.0.0
+2026-03-31 (Date of Last Commit)
+* First version of the QC plotting and filtering pipeline

all_of_us/mitochondria/MitoPostProcessing.wdl

@@ -0,0 +1,102 @@
+version 1.0
+
+struct RuntimeAttr {
+    Float? mem_gb
+    Int? cpu_cores
+    Int? disk_gb
+    Int? preemptible_tries
+    Int? max_retries
+}
+
+workflow MitoPostProcessing {
+    meta {
+        description: "Runs mito post-processing from the cleaned notebook: exports filtered VCF, sample metadata TSV, and all generated plots as SVG."
+        allowNestedInputs: true
+    }
+
+    input {
+        String output_path
+        String input_path
+        String output_base
+
+        String hail_docker = "us.gcr.io/broad-gotc-prod/aou_mitochondria_post:0.0.5"
+        RuntimeAttr? runtime_attr_override
+    }
+
+    String pipeline_version = "aou_9.0.0"
+
+    call RunMitoPostProcessing {
+        input:
+            output_path              = output_path,
+            input_path               = input_path,
+            output_base              = output_base,
+            hail_docker              = hail_docker,
+            runtime_attr_override    = runtime_attr_override
+    }
+
+    output {
+        File filtered_vcf                      = RunMitoPostProcessing.filtered_vcf
+        File filtered_vcf_tbi                  = RunMitoPostProcessing.filtered_vcf_tbi
+        File sample_metadata_tsv               = RunMitoPostProcessing.sample_metadata_tsv
+
+        File variants_per_sample_svg           = RunMitoPostProcessing.variants_per_sample_svg
+        File mito_cn_distribution_svg          = RunMitoPostProcessing.mito_cn_distribution_svg
+        File variant_allele_frequency_svg      = RunMitoPostProcessing.variant_allele_frequency_svg
+        File variant_af_and_allele_fraction_svg = RunMitoPostProcessing.variant_af_and_allele_fraction_svg
+        File numt_fp_by_mtcn_svg               = RunMitoPostProcessing.numt_fp_by_mtcn_svg
+        File haplogroup_heteroplasmy_svg       = RunMitoPostProcessing.haplogroup_heteroplasmy_svg
+        File haplogroup_homoplasmy_svg         = RunMitoPostProcessing.haplogroup_homoplasmy_svg
+    }
+}
+
+task RunMitoPostProcessing {
+    input {
+        String output_path
+        String input_path
+        String output_base
+
+        String hail_docker
+        RuntimeAttr? runtime_attr_override
+    }
+
+    RuntimeAttr runtime_default = object {
+        mem_gb:           32,
+        disk_gb:          200,
+        cpu_cores:        8,
+        preemptible_tries: 0,
+        max_retries:      1
+    }
+    RuntimeAttr runtime_override = select_first([runtime_attr_override, runtime_default])
+
+    command <<<
+        set -euo pipefail
+
+        python3 /opt/mito_plot_filter.py \
+            --input-path  "~{input_path}" \
+            --output-path "~{output_path}" \
+            --output-base "~{output_base}"
+    >>>
+
+    output {
+        File filtered_vcf                       = "~{output_base}.vcf.bgz"
+        File filtered_vcf_tbi                   = "~{output_base}.vcf.bgz.tbi"
+        File sample_metadata_tsv                = "~{output_base}_metadata.tsv"
+
+        File variants_per_sample_svg            = "~{output_base}.variants_per_sample.svg"
+        File mito_cn_distribution_svg           = "~{output_base}.mito_cn_distribution.svg"
+        File variant_allele_frequency_svg       = "~{output_base}.variant_allele_frequency.svg"
+        File variant_af_and_allele_fraction_svg = "~{output_base}.variant_af_and_allele_fraction.svg"
+        File numt_fp_by_mtcn_svg                = "~{output_base}.numt_fp_by_mtcn.svg"
+        File haplogroup_heteroplasmy_svg        = "~{output_base}.haplogroup_heteroplasmy.svg"
+        File haplogroup_homoplasmy_svg          = "~{output_base}.haplogroup_homoplasmy.svg"
+    }
+
+    runtime {
+        memory:        select_first([runtime_override.mem_gb,           runtime_default.mem_gb])           + " GB"
+        disks:         "local-disk " + select_first([runtime_override.disk_gb, runtime_default.disk_gb])   + " SSD"
+        cpu:           select_first([runtime_override.cpu_cores,        runtime_default.cpu_cores])
+        preemptible:   select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries])
+        maxRetries:    select_first([runtime_override.max_retries,      runtime_default.max_retries])
+        docker:        hail_docker
+    }
+}

pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.changelog.md

@@ -1,7 +1,12 @@
+# 0.0.5
+2026-04-03 (Date of Last Commit)
+
+* Add input_qc_version to parent wdl
+
 # 0.0.4
 2026-04-01 (Date of Last Commit)
 
-* Add input_qc_version to parent wdl
+* split out imputed hom ref sites to their own sites only vcf file output
 
 # 0.0.3
 2026-03-25 (Date of Last Commit)