From ad5f93e87d1475bda5c2a35a410cef74f6176fe2 Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 29 Apr 2024 14:21:27 +0200
Subject: [PATCH 1/2] fix: ebfilter expression depends on ann field presence

---
 snappy_wrappers/wrappers/eb_filter/wrapper.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/snappy_wrappers/wrappers/eb_filter/wrapper.py b/snappy_wrappers/wrappers/eb_filter/wrapper.py
index 78147399f..dfd7bfbe1 100644
--- a/snappy_wrappers/wrappers/eb_filter/wrapper.py
+++ b/snappy_wrappers/wrappers/eb_filter/wrapper.py
@@ -15,6 +15,7 @@
 
 step = snakemake.config["pipeline_step"]["name"]
 config = snakemake.config["step_config"][step]
+has_annotation = str(config.get("has_annotation", False))
 
 if "ebfilter_threshold" in config:
     threshold = config.get("ebfilter_threshold", 0)
@@ -86,7 +87,11 @@
     filter=$(echo "$filter" | sed -e "s/^ || //")
     ann="CSQ"
     zgrep -q "^##INFO=<ID=CSQ," {snakemake.input.vcf} || ann="ANN"
-    filter="$filter || $ann ~ \"stream_gene_variant\""
+    if [[ {has_annotation} == "True" ]]; then
+        filter="$filter || $ann ~ \"stream_gene_variant\""
+    else
+        filter="$filter"
+    fi
     {cmd_fetch} \
     | bcftools view \
         -e "$filter" \

From 02508a76f8a7f31aa340aa53a5f1105a0d49d3ef Mon Sep 17 00:00:00 2001
From: Till Hartmann <till.hartmann@bih-charite.de>
Date: Mon, 29 Apr 2024 16:08:13 +0200
Subject: [PATCH 2/2] quote has_annotation

---
 snappy_wrappers/wrappers/eb_filter/wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/snappy_wrappers/wrappers/eb_filter/wrapper.py b/snappy_wrappers/wrappers/eb_filter/wrapper.py
index dfd7bfbe1..983cb5500 100644
--- a/snappy_wrappers/wrappers/eb_filter/wrapper.py
+++ b/snappy_wrappers/wrappers/eb_filter/wrapper.py
@@ -87,7 +87,7 @@
     filter=$(echo "$filter" | sed -e "s/^ || //")
     ann="CSQ"
     zgrep -q "^##INFO=<ID=CSQ," {snakemake.input.vcf} || ann="ANN"
-    if [[ {has_annotation} == "True" ]]; then
+    if [[ '{has_annotation}' == "True" ]]; then
         filter="$filter || $ann ~ \"stream_gene_variant\""
     else
         filter="$filter"