Workaround for GATK-SV annotation bug (#137)

* workaround for GATK-SV annotation
populationgenomics · Apr 8, 2024 · ce5ce69 · ce5ce69
1 parent eb58690
commit ce5ce69
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diff --git a/images.toml b/images.toml
@@ -12,6 +12,7 @@ fastqe = '0.3.1'
 fastqc = '0.11.9'
 fraser = '1.12.1'
 gatk = '4.2.6.1'
+gatk-sv_issue_661 = 'n_a'
 hap-py = '0.3.15'
 haplocheckcli = '64293b3481d52025a01a293f6cc891546c30660e'
 mitoreport = '1.1.0'

diff --git a/images/gatk-sv_issue_661/Dockerfile b/images/gatk-sv_issue_661/Dockerfile
@@ -0,0 +1,5 @@
+FROM australia-southeast1-docker.pkg.dev/cpg-common/images/sv/sv-pipeline:2023-09-13-v0.28.3-beta-af8362e3
+
+ARG VERSION=${VERSION:-n_a}
+
+COPY compute_AFs.py /opt/sv-pipeline/05_annotation/scripts/compute_AFs.py