diff --git a/tests/liftover_test.nf.test.snap b/tests/liftover_test.nf.test.snap
index 7dfaaf1..023d23d 100644
--- a/tests/liftover_test.nf.test.snap
+++ b/tests/liftover_test.nf.test.snap
@@ -3,6 +3,9 @@
         "content": [
             67,
             {
+                "BCFTOOLS_FILTER": {
+                    "bcftools": 1.2
+                },
                 "BCFTOOLS_REHEADER": {
                     "bcftools": 1.18
                 },
@@ -164,6 +167,7 @@
                 "structural/test1/benchmarks/truvari/test1.HG002.delly.tp-comp.vcf.gz",
                 "structural/test1/benchmarks/truvari/test1.HG002.delly.tp-comp.vcf.gz.tbi",
                 "structural/test1/preprocess",
+                "structural/test1/preprocess/test1.filter.filter.vcf",
                 "structural/test1/preprocess/test1.filter.vcf",
                 "structural/test1/stats",
                 "structural/test1/stats/bcftools",
@@ -183,6 +187,7 @@
                 "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-comp.vcf.gz",
                 "structural/test2/benchmarks/truvari/test2.HG002.manta.tp-comp.vcf.gz.tbi",
                 "structural/test2/preprocess",
+                "structural/test2/preprocess/test2.filter.filter.vcf",
                 "structural/test2/preprocess/test2.filter.vcf",
                 "structural/test2/stats",
                 "structural/test2/stats/bcftools",
@@ -193,16 +198,16 @@
             [
                 "HG002.bcftools_stats.txt:md5,7c007a87b5730787e570712e784d3cc3",
                 "HG002_mqc.stats:md5,68681df47b35e3193be03610f5c6e3d6",
-                "test1.delly.bcftools_stats.txt:md5,d32a9bea755d2065e19e88b9159e2502",
-                "test1.delly_mqc.stats:md5,e140ad55975c767578b0dd6aff58ba29",
-                "test2.manta.bcftools_stats.txt:md5,99f8a0b12efa30c6253b44ebfeb9b1d6",
-                "test2.manta_mqc.stats:md5,1d74b41c6b970992e3a39682b0a68e23"
+                "test1.delly.bcftools_stats.txt:md5,aace5a23af8b02f56bcaf03722f9bb50",
+                "test1.delly_mqc.stats:md5,011ad66fec4287d32cb728c40e240c0b",
+                "test2.manta.bcftools_stats.txt:md5,1e700076bd303ee079b23658485eb7d4",
+                "test2.manta_mqc.stats:md5,011ad66fec4287d32cb728c40e240c0b"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-03T15:52:10.533611573"
+        "timestamp": "2025-01-13T14:41:30.39094733"
     }
 }
\ No newline at end of file
diff --git a/tests/liftover_truth.nf.test.snap b/tests/liftover_truth.nf.test.snap
index ef7a85a..b6d9288 100644
--- a/tests/liftover_truth.nf.test.snap
+++ b/tests/liftover_truth.nf.test.snap
@@ -6,6 +6,9 @@
                 "BCFTOOLS_DEDUP": {
                     "bcftools": 1.18
                 },
+                "BCFTOOLS_FILTER": {
+                    "bcftools": 1.2
+                },
                 "BCFTOOLS_MERGE": {
                     "bcftools": 1.2
                 },
@@ -45,9 +48,6 @@
                 "RTGTOOLS_VCFEVAL": {
                     "rtg-tools": "3.12.1"
                 },
-                "TABIX_BGZIP": {
-                    "tabix": "1.19.1"
-                },
                 "TABIX_BGZIPTABIX": {
                     "tabix": "1.19.1"
                 },
@@ -269,6 +269,7 @@
                 "small/test1/benchmarks/rtgtools/test1.HG002.strelka.weighted_roc.tsv.gz",
                 "small/test1/preprocess",
                 "small/test1/preprocess/test1.dedup.sort.vcf.gz",
+                "small/test1/preprocess/test1.norm.filter.vcf",
                 "small/test1/stats",
                 "small/test1/stats/bcftools",
                 "small/test1/stats/bcftools/test1.strelka.bcftools_stats.txt",
@@ -302,6 +303,7 @@
                 "small/test2/benchmarks/rtgtools/test2.HG002.bcftools.weighted_roc.tsv.gz",
                 "small/test2/preprocess",
                 "small/test2/preprocess/test2.dedup.sort.vcf.gz",
+                "small/test2/preprocess/test2.norm.filter.vcf",
                 "small/test2/stats",
                 "small/test2/stats/bcftools",
                 "small/test2/stats/bcftools/test2.bcftools.bcftools_stats.txt"
@@ -325,16 +327,16 @@
                 "suffixpointer0:md5,468281ffb10d7dd934289af762a03781",
                 "HG002.sort.merged.bed:md5,5e997133249c2227cb5363b314245636",
                 "HG002.bcftools_stats.txt:md5,07fafa430abc857969015ea6a41d1032",
-                "test1.HG002.strelka.extended.csv:md5,fadf06276179c1cc388007e5651fb9af",
-                "test1.HG002.strelka.roc.Locations.INDEL.PASS.csv.gz:md5,a08665be8ea20855a14d6418d07521dc",
-                "test1.HG002.strelka.roc.Locations.INDEL.csv.gz:md5,8d4a20a5914379230952aeb252845e2d",
-                "test1.HG002.strelka.roc.Locations.SNP.PASS.csv.gz:md5,c546609a3e23b4c5c97ee0fc2e864e07",
-                "test1.HG002.strelka.roc.Locations.SNP.csv.gz:md5,8d2600c17665ed1299e2dd483705ddaa",
-                "test1.HG002.strelka.roc.all.csv.gz:md5,d0a4408438b2182cb82caec918c090f1",
-                "test1.HG002.strelka.summary.csv:md5,001fa2371777d1d2dc3eb0f4dcaca197",
-                "test1.HG002.strelka.phasing.txt:md5,0c9340e64e032b5f74d0ea3773464afd",
-                "test1.HG002.strelka.summary.txt:md5,4b775edb878759727ef66d5d5b2b9ee8",
-                "test1.strelka.bcftools_stats.txt:md5,f9f8cf5c1be9c88754888ef8cbfb06f4",
+                "test1.HG002.strelka.extended.csv:md5,111a236ca6b747face70e8111c09c51f",
+                "test1.HG002.strelka.roc.Locations.INDEL.PASS.csv.gz:md5,5425b34f4688dda4d55f9f7a73667b18",
+                "test1.HG002.strelka.roc.Locations.INDEL.csv.gz:md5,eb9834ec5660d1e32ade0c856b9cfb7c",
+                "test1.HG002.strelka.roc.Locations.SNP.PASS.csv.gz:md5,778eb91f54cb830fb91fcddc688668e0",
+                "test1.HG002.strelka.roc.Locations.SNP.csv.gz:md5,516a4b58814cf32245a5b2f2c0445c8e",
+                "test1.HG002.strelka.roc.all.csv.gz:md5,a69fb6ae5cd051d4607da0224009f1d1",
+                "test1.HG002.strelka.summary.csv:md5,d29cba645e161dbdeb6247f57fce5780",
+                "test1.HG002.strelka.phasing.txt:md5,38920536b8c3e241e873c07ba61762e6",
+                "test1.HG002.strelka.summary.txt:md5,6c43a0d1ad065f851942828259d551a5",
+                "test1.strelka.bcftools_stats.txt:md5,7d65792aa3a84de09675facf62135c93",
                 "test2.HG002.bcftools.extended.csv:md5,05c6efd85a9b9823a5ddfe6619be3323",
                 "test2.HG002.bcftools.roc.Locations.INDEL.PASS.csv.gz:md5,463cee548b7bdf133c0ae9b5803a50ca",
                 "test2.HG002.bcftools.roc.Locations.INDEL.csv.gz:md5,424e39c327ae6ef9001942bc895abdc9",
@@ -348,9 +350,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-10T10:20:35.930923969"
+        "timestamp": "2025-01-13T14:48:00.444469734"
     }
 }
\ No newline at end of file
diff --git a/tests/somatic_indel.nf.test.snap b/tests/somatic_indel.nf.test.snap
index 1f04021..5f59ce6 100644
--- a/tests/somatic_indel.nf.test.snap
+++ b/tests/somatic_indel.nf.test.snap
@@ -3,6 +3,9 @@
         "content": [
             27,
             {
+                "BCFTOOLS_FILTER": {
+                    "bcftools": 1.2
+                },
                 "BCFTOOLS_REHEADER": {
                     "bcftools": 1.18
                 },
@@ -33,9 +36,6 @@
                 "PLOTS": {
                     "r-base": "4.3.1"
                 },
-                "TABIX_BGZIP": {
-                    "tabix": "1.19.1"
-                },
                 "TABIX_BGZIPTABIX": {
                     "tabix": "1.19.1"
                 },
@@ -150,6 +150,8 @@
                 "indel/test1/benchmarks/sompy/test1.SEQC2.freebayes.features.csv",
                 "indel/test1/benchmarks/sompy/test1.SEQC2.freebayes.metrics.json",
                 "indel/test1/benchmarks/sompy/test1.SEQC2.freebayes.stats.csv",
+                "indel/test1/preprocess",
+                "indel/test1/preprocess/test1.filter.vcf",
                 "indel/test1/stats",
                 "indel/test1/stats/bcftools",
                 "indel/test1/stats/bcftools/test1.freebayes.bcftools_stats.txt",
@@ -161,6 +163,7 @@
                 "indel/test2/benchmarks/sompy/test2.SEQC2.strelka.stats.csv",
                 "indel/test2/preprocess",
                 "indel/test2/preprocess/HCC1395T_vs_HCC1395N.strelka.somatic_indels.sort.vcf.gz",
+                "indel/test2/preprocess/test2.filter.vcf",
                 "indel/test2/stats",
                 "indel/test2/stats/bcftools",
                 "indel/test2/stats/bcftools/test2.strelka.bcftools_stats.txt",
@@ -170,13 +173,13 @@
             [
                 "SEQC2.bcftools_stats.txt:md5,e530daf4f6a4923f1cd85c51893d5747",
                 "test1.freebayes.bcftools_stats.txt:md5,c5025b5c6256c1d808badee73a7c220c",
-                "test2.strelka.bcftools_stats.txt:md5,ec553881bc70c786e8cec95192823634"
+                "test2.strelka.bcftools_stats.txt:md5,1e700076bd303ee079b23658485eb7d4"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-10T11:27:48.141030523"
+        "timestamp": "2025-01-13T14:32:00.898226798"
     }
 }
\ No newline at end of file