Merge pull request #415 from genomic-medicine-sweden/soft_filter_fix

fix: avoid clash with earlier filter annotation
genomic-medicine-sweden · Feb 26, 2024 · 0938808 · 0938808
2 parents 5871486 + 03e0a0e
commit 0938808
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diff --git a/config/filters/config_soft_filter_umi_vep105.yaml b/config/filters/config_soft_filter_umi_vep105.yaml
@@ -12,7 +12,7 @@ filters:
   germline:
     description: "Hard filter germline"
     expression: "(VEP:gnomAD_AF > 0.005)"
-    soft_filter_flag: "germline"
+    soft_filter_flag: "germline_gnomad"
     soft_filter: "True"
   af_snv:
     description: "Hard filter SNV variants with low vaf"

diff --git a/requirements.txt b/requirements.txt
@@ -8,3 +8,4 @@ drmaa
 cyvcf2==0.30.16
 tabulate<0.9.0
 pulp<2.8
+smart_open<7.0.0