From 2cbb303848a2375377e512fa215ace41ada6ebbd Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Fri, 7 Feb 2025 13:14:41 -0500
Subject: [PATCH] Integrated new params into makegq/concordance workflow

---
 .github/.dockstore.yml                        |  1 +
 ...akeGqRecalibratorTrainingSetFromPacBio.wdl | 18 +++++++++++++++++
 wdl/SVConcordance.wdl                         | 20 ++++++++++++++++++-
 wdl/SVConcordancePacBioSample.wdl             |  9 +++++++++
 4 files changed, 47 insertions(+), 1 deletion(-)

diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
index 17ddd07c2..d42f09cd6 100644
--- a/.github/.dockstore.yml
+++ b/.github/.dockstore.yml
@@ -175,6 +175,7 @@ workflows:
     filters:
       branches:
         - main
+        - kj_dragensv_benchmarking
       tags:
         - /.*/
 
diff --git a/wdl/MakeGqRecalibratorTrainingSetFromPacBio.wdl b/wdl/MakeGqRecalibratorTrainingSetFromPacBio.wdl
index 61dc1e309..49a8aaeb6 100644
--- a/wdl/MakeGqRecalibratorTrainingSetFromPacBio.wdl
+++ b/wdl/MakeGqRecalibratorTrainingSetFromPacBio.wdl
@@ -44,10 +44,20 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
     Float? pesr_size_similarity_strict = 0.5
     Int? pesr_breakend_window_strict = 5000
 
+    File? clustering_config_strict
+    File? stratification_config_strict
+    Array[String]? track_names_strict
+    Array[File]? track_intervals_strict
+
     Float? pesr_interval_overlap_loose = 0
     Float? pesr_size_similarity_loose = 0
     Int? pesr_breakend_window_loose = 5000
 
+    File? clustering_config_loose
+    File? stratification_config_loose
+    Array[String]? track_names_loose
+    Array[File]? track_intervals_loose
+
     File reference_dict
 
     String sv_utils_docker
@@ -184,6 +194,10 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
         pesr_interval_overlap=pesr_interval_overlap_loose,
         pesr_size_similarity=pesr_size_similarity_loose,
         pesr_breakend_window=pesr_breakend_window_loose,
+        clustering_config = clustering_config_loose,
+        stratification_config = stratification_config_loose,
+        track_names = track_names_loose,
+        track_intervals = track_intervals_loose,
         sv_base_mini_docker=sv_base_mini_docker,
         sv_pipeline_docker=sv_pipeline_docker,
         gatk_docker=gatk_docker,
@@ -201,6 +215,10 @@ workflow MakeGqRecalibratorTrainingSetFromPacBio {
         pesr_interval_overlap=pesr_interval_overlap_strict,
         pesr_size_similarity=pesr_size_similarity_strict,
         pesr_breakend_window=pesr_breakend_window_strict,
+        clustering_config = clustering_config_strict,
+        stratification_config = stratification_config_strict,
+        track_names = track_names_strict,
+        track_intervals = track_intervals_strict,
         sv_base_mini_docker=sv_base_mini_docker,
         sv_pipeline_docker=sv_pipeline_docker,
         gatk_docker=gatk_docker,
diff --git a/wdl/SVConcordance.wdl b/wdl/SVConcordance.wdl
index c99b01100..b0bc9fe70 100644
--- a/wdl/SVConcordance.wdl
+++ b/wdl/SVConcordance.wdl
@@ -13,6 +13,12 @@ workflow SVConcordance {
     File contig_list
     File reference_dict
 
+    # Reclustering parameters
+    File? clustering_config
+    File? stratification_config
+    Array[String]? track_names
+    Array[File]? track_intervals
+
     String gatk_docker
     String sv_base_mini_docker
 
@@ -30,6 +36,10 @@ workflow SVConcordance {
         truth_vcf=truth_vcf,
         output_prefix="~{output_prefix}.concordance.~{contig}.unsorted",
         contig=contig,
+        clustering_config=clustering_config,
+        stratification_config=stratification_config,
+        track_names=track_names,
+        track_bed_files=track_bed_files,
         reference_dict=reference_dict,
         java_mem_fraction=java_mem_fraction,
         gatk_docker=gatk_docker,
@@ -68,6 +78,10 @@ task SVConcordanceTask {
     String output_prefix
     File reference_dict
     String? contig
+    File? clustering_config
+    File? stratification_config
+    Array[String]? track_names
+    Array[File]? track_intervals
     String? additional_args
 
     Float? java_mem_fraction
@@ -120,6 +134,10 @@ task SVConcordanceTask {
       --eval ~{eval_vcf} \
       --truth ~{truth_vcf} \
       -O ~{output_prefix}.vcf.gz \
+      ~{if defined(clustering_config) then "--clustering-config " + clustering_config else ""} \
+      ~{if defined(stratification_config) then "--stratify-config " + stratification_config else ""} \
+      ~{if defined(track_names) then "--track-name " + sep(" --track-name ", track_names) else ""} \
+      ~{if defined(track_intervals) then "--track-intervals " + sep(" --track-intervals ", track_intervals) else ""} \
       --do-not-sort \
       ~{additional_args}
   >>>
@@ -132,4 +150,4 @@ task SVConcordanceTask {
     preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
     maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
   }
-}
+}
\ No newline at end of file
diff --git a/wdl/SVConcordancePacBioSample.wdl b/wdl/SVConcordancePacBioSample.wdl
index 2f962c09d..ba7e32343 100644
--- a/wdl/SVConcordancePacBioSample.wdl
+++ b/wdl/SVConcordancePacBioSample.wdl
@@ -20,6 +20,11 @@ workflow SVConcordancePacBioSample {
     Float? pesr_size_similarity
     Int? pesr_breakend_window
 
+    File? clustering_config
+    File? stratification_config
+    Array[String]? track_names
+    Array[File]? track_intervals
+
     File reference_dict
 
     # For debugging
@@ -57,6 +62,10 @@ workflow SVConcordancePacBioSample {
         eval_vcf=sample_vcf,
         output_prefix="~{prefix}.concordance.~{tool_names[i]}.~{sample_id}.unsorted",
         additional_args="--pesr-interval-overlap ~{pesr_interval_overlap} --pesr-size-similarity ~{pesr_size_similarity} --pesr-breakend-window ~{pesr_breakend_window}",
+        clustering_config=clustering_config,
+        stratification_config=stratification_config,
+        track_names=track_names,
+        track_intervals=track_intervals,
         reference_dict=reference_dict,
         java_mem_fraction=java_mem_fraction,
         gatk_docker=gatk_docker,