From 4f968dea3e03411a04fd41116e779a488119b390 Mon Sep 17 00:00:00 2001
From: Nick Smith <nhsmith@stanford.edu>
Date: Thu, 16 Jul 2026 10:49:24 -0700
Subject: [PATCH 1/2] preliminary CL upload

---
 config/config.yaml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/config/config.yaml b/config/config.yaml
index 0f90f7c..da0d213 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -762,6 +762,21 @@ variant-calls:
       filename: A006850052_NA12878_200M_BWA_DV_STANDART.vcf
     benchmark: giab-NA12878-agilent-200M
     rename-contigs: true
+  strelka_default-75M-agilent:
+    labels:
+      site: CL
+      pipeline: strelka-default
+      trimming: FastP v0.23.4
+      read-mapping: BWA_MEM docker-pcapcore_5.6.1
+      variant-detection:  strelka2 v2.9.10
+      genotyping: none
+      reads: 75M
+    subcategory: NA12878-agilent
+    zenodo:
+      deposition: 21399917
+      filename: BWA_STRELKA_PASS.vcf.gz
+    benchmark: giab-NA12878-agilent-75M
+    rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
 custom-benchmarks:
   giab-NA12878-agilent-200M:
     zenodo:

From df33f5f57d7dd31da25f9c1db26919f220a903b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20B=C3=A4uerle?=
 <45968370+famosab@users.noreply.github.com>
Date: Mon, 10 Aug 2026 10:41:15 +0200
Subject: [PATCH 2/2] Update config/config.yaml

---
 config/config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/config.yaml b/config/config.yaml
index da0d213..6391d47 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -776,7 +776,7 @@ variant-calls:
       deposition: 21399917
       filename: BWA_STRELKA_PASS.vcf.gz
     benchmark: giab-NA12878-agilent-75M
-    rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
+    rename-contigs: true
 custom-benchmarks:
   giab-NA12878-agilent-200M:
     zenodo: