diff --git a/CHANGELOG.md b/CHANGELOG.md
index 34faf3bc..93621036 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 1. Added the samplesheet to the pipeline output as `OUTDIR/samplesheet.csv`
 2. Added the `--bedpe` parameter. This makes the pipeline output BEDPE files alongside the VCF files.
 3. Added parallelization on SV type to the delly flow
+4. Added a `--gtf` parameter for annotation of gene and transcript overlap using `gatk SVAnnotate`.
 
 ### `Changes`
 
diff --git a/assets/svync/delly.yaml b/assets/svync/delly.yaml
index 55d1c5d8..45f4ca12 100644
--- a/assets/svync/delly.yaml
+++ b/assets/svync/delly.yaml
@@ -1,6 +1,8 @@
 id: delly_$INFO/SVTYPE
 alt:
-  BND: TRA
+  alts:
+    BND: <TRA>
+  value: <$INFO/SVTYPE>
 info:
   CALLERS:
     value: delly
diff --git a/assets/svync/manta.yaml b/assets/svync/manta.yaml
index d081ef29..440618a4 100644
--- a/assets/svync/manta.yaml
+++ b/assets/svync/manta.yaml
@@ -1,4 +1,6 @@
 id: manta_$INFO/SVTYPE
+alt:
+  value: <$INFO/SVTYPE>
 info:
   CALLERS:
     value: manta
diff --git a/bin/preprocess_gtf.py b/bin/preprocess_gtf.py
new file mode 100755
index 00000000..c252cd05
--- /dev/null
+++ b/bin/preprocess_gtf.py
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+# https://github.com/broadinstitute/gatk-sv/blob/main/scripts/inputs/preprocess_gtf.py
+
+"""
+Preprocess GENCODE basic GTF to extract canonical protein-coding transcripts for functional consequence annotation.
+"""
+
+import argparse
+import gzip
+
+
+CHROM_FIELD = 0
+ELEMENT_FIELD = 2
+ATTRIBUTES_FIELD = 8
+TRANSCRIPT_TYPES = {"protein_coding", "nonsense_mediated_decay"}
+CANONICAL = {"MANE_Plus_Clinical", "MANE_Select", "Ensembl_canonical"}
+
+
+# Flexibly open .gz or uncompressed file to read
+def _open(filename):
+    if filename.endswith(".gz"):
+        return gzip.open(filename, 'rt')
+    else:
+        return open(filename, 'r')
+
+
+# Extract transcript type and canonical status
+def parse_attributes(field):
+    # format: key1 "value1"; key2 "value2";
+    # keys may be repeated so cannot convert directly to dictionary
+    attributes_list = [tuple(x.replace('"', '').split(' ')) for x in field.rstrip(";").split("; ")]
+    protein = False
+    canonical = False
+    for key, val in attributes_list:
+        if key == "tag" and val in CANONICAL:
+            canonical = True
+        elif key == "transcript_type" and val in TRANSCRIPT_TYPES:
+            protein = True
+    return protein, canonical
+
+
+def process(gtf, outfile):
+    with _open(gtf) as inp, open(outfile, 'w') as out:
+        gene_line = ""
+        for line in inp:
+            if line.startswith("#"):
+                continue
+            fields = line.rstrip('\n').split('\t')
+
+            # Drop mitochondria
+            if fields[CHROM_FIELD] == 'chrM':
+                continue
+
+            # Store gene line to print if transcript is eligible
+            if fields[ELEMENT_FIELD] == "gene":
+                gene_line = line
+                continue
+
+            # Select protein-coding and canonical transcripts only
+            protein, canonical = parse_attributes(fields[ATTRIBUTES_FIELD])
+            if protein and canonical:
+                out.write(gene_line + line)
+                gene_line = ""  # only print gene line before first transcript line
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('gtf', help="Input GTF from GENCODE")
+    parser.add_argument('outfile', help="Output filename")
+    args = parser.parse_args()
+
+    process(args.gtf, args.outfile)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/conf/modules.config b/conf/modules.config
index ed24085e..378a340d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -259,6 +259,10 @@ process {
         ext.args = "-ends"
     }
 
+    withName: "^.*GATK4_SVANNOTATE\$" {
+        ext.prefix = {"${meta.id}.${meta.variant_type}.svannotate"}
+    }
+
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         SV AND CNV FILTERING
diff --git a/conf/test.config b/conf/test.config
index 3d807df7..a9672f77 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -33,6 +33,8 @@ params {
     // Fasta references
     fasta                   = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.fasta"
     fai                     = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.fasta.fai"
+    dict                    = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.dict"
+    gtf                     = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.gtf"
     // bwa                     = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/bwa.tar.gz"
     expansionhunter_catalog = params.test_data["homo_sapiens"]["genome"]["expansionhunter"]
     qdnaseq_male            = params.test_data["homo_sapiens"]["genome"]["genome_qdnaseq"]
diff --git a/main.nf b/main.nf
index 065e57f2..945f1d6f 100644
--- a/main.nf
+++ b/main.nf
@@ -28,6 +28,8 @@ include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_stru
 
 params.fasta                    = getGenomeAttribute('fasta')
 params.fai                      = getGenomeAttribute('fai')
+params.dict                     = getGenomeAttribute('dict')
+params.gtf                      = getGenomeAttribute('gtf')
 params.vep_cache                = getGenomeAttribute('vep_cache')
 // params.bwa                      = getGenomeAttribute('bwa')
 params.annotsv_annotations      = getGenomeAttribute('annotsv_annotations')
@@ -81,6 +83,8 @@ workflow {
         // files
         params.fasta,
         params.fai,
+        params.dict,
+        params.gtf,
         params.expansionhunter_catalog ?: "https://github.com/Illumina/ExpansionHunter/raw/master/variant_catalog/grch38/variant_catalog.json",
         params.qdnaseq_female,
         params.qdnaseq_male,
diff --git a/modules.json b/modules.json
index f21c7565..3a02a14a 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "annotsv/annotsv": {
                         "branch": "master",
-                        "git_sha": "a94ad45fa5b350961c374c46f79bc86cd5853353",
+                        "git_sha": "296d216c3f6384936a6526b6fbed7e6412259fb4",
                         "installed_by": ["modules"]
                     },
                     "annotsv/installannotations": {
                         "branch": "master",
-                        "git_sha": "a94ad45fa5b350961c374c46f79bc86cd5853353",
+                        "git_sha": "296d216c3f6384936a6526b6fbed7e6412259fb4",
                         "installed_by": ["modules"]
                     },
                     "bcftools/annotate": {
@@ -66,6 +66,16 @@
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
                         "installed_by": ["modules"]
                     },
+                    "gatk4/createsequencedictionary": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": ["modules"]
+                    },
+                    "gatk4/svannotate": {
+                        "branch": "master",
+                        "git_sha": "cc7e281e7877146dac79c5a484e6e2b10086234a",
+                        "installed_by": ["modules"]
+                    },
                     "gawk": {
                         "branch": "master",
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
@@ -135,7 +145,7 @@
                     },
                     "svync": {
                         "branch": "master",
-                        "git_sha": "916a4cbc4f831d501860495b157c4857833e22a7",
+                        "git_sha": "0fc190096fa8dcc9878cef178479f22e03f174a1",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
diff --git a/modules/local/preprocess_gtf/environment.yml b/modules/local/preprocess_gtf/environment.yml
new file mode 100644
index 00000000..519d3a96
--- /dev/null
+++ b/modules/local/preprocess_gtf/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::python=3.13.5
diff --git a/modules/local/preprocess_gtf/main.nf b/modules/local/preprocess_gtf/main.nf
new file mode 100644
index 00000000..d140ef8a
--- /dev/null
+++ b/modules/local/preprocess_gtf/main.nf
@@ -0,0 +1,40 @@
+process PREPROCESS_GTF {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8a/8ad257d53c2a2b8810d2b12d4d8e3ea438bc8c4a6be7c39b0354cd7bb8d5c260/data':
+        'community.wave.seqera.io/library/python:3.13.5--18032a8dc5d4b91e' }"
+
+    input:
+    tuple val(meta), path(gtf)
+
+    output:
+    tuple val(meta), path("*.sanitized.gtf"), emit: gtf
+    path "versions.yml"                     , emit: versions
+
+    script:
+    def prefix  = task.ext.prefix ?: "${gtf.baseName}"
+
+    """
+    preprocess_gtf.py $gtf ${prefix}.sanitized.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        grep: \$(echo \$(grep --version) | sed -e 's/grep (GNU grep) //;s/ Copyright.*//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${gtf.baseName}"
+
+    """
+    touch ${prefix}.sanitized.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        grep: \$(echo \$(grep --version) | sed -e 's/grep (GNU grep) //;s/ Copyright.*//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/annotsv/annotsv/annotsv-annotsv.diff b/modules/nf-core/annotsv/annotsv/annotsv-annotsv.diff
deleted file mode 100644
index a9c3fe23..00000000
--- a/modules/nf-core/annotsv/annotsv/annotsv-annotsv.diff
+++ /dev/null
@@ -1,45 +0,0 @@
-Changes in module 'nf-core/annotsv/annotsv'
---- modules/nf-core/annotsv/annotsv/main.nf
-+++ modules/nf-core/annotsv/annotsv/main.nf
-@@ -17,7 +17,7 @@
-     output:
-     tuple val(meta), path("*.tsv")              , emit: tsv
-     tuple val(meta), path("*.unannotated.tsv")  , emit: unannotated_tsv, optional: true
--    tuple val(meta), path("*.vcf")              , emit: vcf, optional: true
-+    tuple val(meta), path("*.vcf")              , emit: vcf
-     path "versions.yml"                         , emit: versions
- 
-     when:
-@@ -39,11 +39,15 @@
-         ${small_variants} \\
-         ${fp_snv} \\
-         ${transcripts} \\
--        -outputFile ${prefix}.tsv \\
-+        -outputFile ${prefix}.raw.tsv \\
-         -SVinputFile ${sv_vcf} \\
-         ${args}
- 
-     mv *_AnnotSV/* .
-+    awk 'BEGIN { FS=OFS="\t" } { if (NR > 1 && NF >= 8) \$1 = \$1 "_" NR; print }' ${prefix}.raw.tsv > ${prefix}.tsv
-+
-+    variantconvert convert -i ${prefix}.tsv -o ${prefix}.vcf -fi annotsv -fo vcf -c /usr/local/share/python3/variantconvert/configs/GRCh38/annotsv3_from_vcf.json
-+    sed -i 's/contig=<ID=MT/contig=<ID=M/' ${prefix}.vcf
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-@@ -55,12 +59,10 @@
-     def args = task.ext.args ?: ''
-     def prefix = task.ext.prefix ?: "${meta.id}"
- 
--    def create_vcf = args.contains("-vcf 1") ? "touch ${prefix}.vcf" : ""
--
-     """
-     touch ${prefix}.tsv
-     touch ${prefix}.unannotated.tsv
--    ${create_vcf}
-+    touch ${prefix}.vcf
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-
-************************************************************
diff --git a/modules/nf-core/annotsv/annotsv/environment.yml b/modules/nf-core/annotsv/annotsv/environment.yml
index e5f4a3e4..d8f5ae51 100644
--- a/modules/nf-core/annotsv/annotsv/environment.yml
+++ b/modules/nf-core/annotsv/annotsv/environment.yml
@@ -1,7 +1,7 @@
-name: annotsv_annotsv
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::annotsv=3.4.2
+  - bioconda::annotsv=3.4.6
diff --git a/modules/nf-core/annotsv/annotsv/main.nf b/modules/nf-core/annotsv/annotsv/main.nf
index e9d47db7..63eeab67 100644
--- a/modules/nf-core/annotsv/annotsv/main.nf
+++ b/modules/nf-core/annotsv/annotsv/main.nf
@@ -4,8 +4,11 @@ process ANNOTSV_ANNOTSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/df/df5e87ce610d595afe5f1e4017c255e53590cfa9b156c43310d637b36bfd12b3/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.6--c5a6da1bf4c2c8e5' }"
+
+    // Container options are needed to allow AnnotSV to overwrite a file in a dependency directory in Singularity
+    containerOptions "${ workflow.containerEngine == 'singularity' ? '--writable-tmpfs' : ''}"
 
     input:
     tuple val(meta), path(sv_vcf), path(sv_vcf_index), path(candidate_small_variants)
@@ -15,10 +18,10 @@ process ANNOTSV_ANNOTSV {
     tuple val(meta5), path(gene_transcripts)
 
     output:
-    tuple val(meta), path("*.tsv")              , emit: tsv
-    tuple val(meta), path("*.unannotated.tsv")  , emit: unannotated_tsv, optional: true
-    tuple val(meta), path("*.vcf")              , emit: vcf, optional: true
-    path "versions.yml"                         , emit: versions
+    tuple val(meta), path("*.tsv")            , emit: tsv
+    tuple val(meta), path("*.unannotated.tsv"), emit: unannotated_tsv, optional: true
+    tuple val(meta), path("*.vcf")            , emit: vcf            , optional: true
+    path "versions.yml"                       , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +30,10 @@ process ANNOTSV_ANNOTSV {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def cand_genes = candidate_genes ? "-candidateGenesFile ${candidate_genes}" : ""
+    def cand_genes     = candidate_genes          ? "-candidateGenesFile ${candidate_genes}"              : ""
     def small_variants = candidate_small_variants ? "-candidateSnvIndelFiles ${candidate_small_variants}" : ""
-    def fp_snv = false_positive_snv ? "-snvIndelFiles ${false_positive_snv}" : ""
-    def transcripts = gene_transcripts ? "-txFile ${gene_transcripts}" : ""
+    def fp_snv         = false_positive_snv       ? "-snvIndelFiles ${false_positive_snv}"                : ""
+    def transcripts    = gene_transcripts         ? "-txFile ${gene_transcripts}"                         : ""
 
     """
     AnnotSV \\
@@ -52,14 +55,12 @@ process ANNOTSV_ANNOTSV {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     def create_vcf = args.contains("-vcf 1") ? "touch ${prefix}.vcf" : ""
 
     """
-    echo "$args"
-
     touch ${prefix}.tsv
     touch ${prefix}.unannotated.tsv
     ${create_vcf}
diff --git a/modules/nf-core/annotsv/annotsv/meta.yml b/modules/nf-core/annotsv/annotsv/meta.yml
index f690f0aa..1ba4feaf 100644
--- a/modules/nf-core/annotsv/annotsv/meta.yml
+++ b/modules/nf-core/annotsv/annotsv/meta.yml
@@ -14,80 +14,118 @@ tools:
       tool_dev_url: "https://github.com/lgmgeo/AnnotSV"
       doi: 10.1093/bioinformatics/bty304
       licence: ["GPL-3.0"]
+      identifier: biotools:AnnotSV
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - sv_vcf:
-      type: file
-      description: A VCF or BED file containing the structural variants to be annotated
-      pattern: "*.{bed,vcf,vcf.gz}"
-  - sv_vcf_index:
-      type: file
-      description: OPTIONAL - The index for gzipped VCF files
-      pattern: "*.tbi"
-  - candidate_small_variants:
-      type: file
-      description: OPTIONAL - A file containing candidate small variants
-      pattern: "*.{vcf,vcf.gz}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing annotations information
-  - annotations:
-      type: directory
-      description: |
-        The directory containing the annotations (URL to download this will be made available soon)
-        For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation)
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing candidate genes information
-  - candidate_genes:
-      type: file
-      description: OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated)
-      pattern: "*.txt"
-  - meta4:
-      type: map
-      description: |
-        Groovy Map containing candidate false positive SNV information
-  - false_positive_snv:
-      type: file
-      description: OPTIONAL - A VCF file containing small variant candidates
-      pattern: "*.{vcf,vcf.gz}"
-  - meta5:
-      type: map
-      description: |
-        Groovy Map containing candidate gene transcripts information
-  - gene_transcripts:
-      type: file
-      description: OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated)
-      pattern: "*.txt"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - sv_vcf:
+        type: file
+        description: A VCF or BED file containing the structural variants to be annotated
+        pattern: "*.{bed,vcf,vcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003" # BED
+          - edam: "http://edamontology.org/format_3016" # VCF
+    - sv_vcf_index:
+        type: file
+        description: OPTIONAL - The index for gzipped VCF files
+        pattern: "*.tbi"
+        ontologies:
+          - edam: "http://edamontology.org/format_3475" # Tabix index
+    - candidate_small_variants:
+        type: file
+        description: OPTIONAL - A file containing candidate small variants
+        pattern: "*.{vcf,vcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016" # VCF
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing annotations information
+    - annotations:
+        type: directory
+        description: |
+          The directory containing the annotations (URL to download this will be made available soon)
+          For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation)
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing candidate genes information
+    - candidate_genes:
+        type: file
+        description: OPTIONAL - A file containing genes (either space-separated, tab-separated
+          or line-break-separated)
+        pattern: "*.txt"
+        ontologies:
+          - edam: "http://edamontology.org/format_2330" # Text file
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing candidate false positive SNV information
+    - false_positive_snv:
+        type: file
+        description: OPTIONAL - A VCF file containing small variant candidates
+        pattern: "*.{vcf,vcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016" # VCF
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing candidate gene transcripts information
+    - gene_transcripts:
+        type: file
+        description: OPTIONAL - A file containing the preferred gene transcripts to
+          be used in priority during annotation (either space-separated or tab-separated)
+        pattern: "*.txt"
+        ontologies:
+          - edam: "http://edamontology.org/format_2330" # Text file
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - tsv:
-      type: file
-      description: A TSV file containing the annotated variants
-      pattern: "*.tsv"
-  - unannotated_tsv:
-      type: file
-      description: OPTIONAL - TSV file containing the unannotated variants
-      pattern: "*.unannotated.tsv"
-  - vcf:
-      type: file
-      description: |
-        OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args)
-      pattern: "*.vcf"
+  tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.tsv":
+          type: file
+          description: A TSV file containing the annotated variants
+          pattern: "*.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475" # TSV
+  unannotated_tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.unannotated.tsv":
+          type: file
+          description: OPTIONAL - TSV file containing the unannotated variants
+          pattern: "*.unannotated.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475" # TSV
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.vcf":
+          type: file
+          description: |
+            OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args)
+          pattern: "*.vcf"
+          ontologies:
+            - edam: "http://edamontology.org/format_3016" # VCF
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
 authors:
   - "@nvnieuwk"
 maintainers:
diff --git a/modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap b/modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap
index fd46d7e7..53516807 100644
--- a/modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap
+++ b/modules/nf-core/annotsv/annotsv/tests/main.nf.test.snap
@@ -25,7 +25,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,a5c7d9d19db00a62006faa1bafa917ec"
+                    "versions.yml:md5,8538f3187cc91433cef9d3db1850fbb1"
                 ],
                 "tsv": [
                     [
@@ -50,14 +50,14 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,a5c7d9d19db00a62006faa1bafa917ec"
+                    "versions.yml:md5,8538f3187cc91433cef9d3db1850fbb1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-05-29T15:10:39.33144868"
+        "timestamp": "2025-07-10T16:46:10.783184639"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/annotsv/annotsv/tests/tags.yml b/modules/nf-core/annotsv/annotsv/tests/tags.yml
deleted file mode 100644
index 54453426..00000000
--- a/modules/nf-core/annotsv/annotsv/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-annotsv/annotsv:
-  - "modules/nf-core/annotsv/annotsv/**"
diff --git a/modules/nf-core/annotsv/installannotations/environment.yml b/modules/nf-core/annotsv/installannotations/environment.yml
index b759f91d..d8f5ae51 100644
--- a/modules/nf-core/annotsv/installannotations/environment.yml
+++ b/modules/nf-core/annotsv/installannotations/environment.yml
@@ -1,7 +1,7 @@
-name: annotsv_installannotations
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::annotsv=3.4.2
+  - bioconda::annotsv=3.4.6
diff --git a/modules/nf-core/annotsv/installannotations/main.nf b/modules/nf-core/annotsv/installannotations/main.nf
index 371e1bbf..147bbc12 100644
--- a/modules/nf-core/annotsv/installannotations/main.nf
+++ b/modules/nf-core/annotsv/installannotations/main.nf
@@ -4,8 +4,8 @@ process ANNOTSV_INSTALLANNOTATIONS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/df/df5e87ce610d595afe5f1e4017c255e53590cfa9b156c43310d637b36bfd12b3/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.6--c5a6da1bf4c2c8e5' }"
 
     output:
     path "AnnotSV_annotations", emit: annotations
diff --git a/modules/nf-core/annotsv/installannotations/meta.yml b/modules/nf-core/annotsv/installannotations/meta.yml
index a04c4f1d..670c7150 100644
--- a/modules/nf-core/annotsv/installannotations/meta.yml
+++ b/modules/nf-core/annotsv/installannotations/meta.yml
@@ -12,15 +12,22 @@ tools:
       documentation: "https://lbgi.fr/AnnotSV/"
       tool_dev_url: "https://github.com/lgmgeo/AnnotSV"
       licence: ["GPL v3"]
+      identifier: biotools:AnnotSV
 output:
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - annotations:
-      type: file
-      description: A folder containing the annotations
-      pattern: "AnnotSV_annotations"
+  annotations:
+    - AnnotSV_annotations:
+        type: file
+        description: A folder containing the annotations
+        pattern: "AnnotSV_annotations"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
 authors:
   - "@nvnieuwk"
 maintainers:
diff --git a/modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap b/modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap
index bb45f1bd..bc1a43d7 100644
--- a/modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap
+++ b/modules/nf-core/annotsv/installannotations/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d0b3dc5e0199653fd81ffd3754e65f9c"
+                    "versions.yml:md5,a7ab4be6d37013bd8c0ca0e388c0a4ee"
                 ],
                 "annotations": [
                     [
@@ -16,14 +16,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d0b3dc5e0199653fd81ffd3754e65f9c"
+                    "versions.yml:md5,a7ab4be6d37013bd8c0ca0e388c0a4ee"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-05-29T15:14:54.723053976"
+        "timestamp": "2025-07-10T16:55:38.662275457"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/annotsv/installannotations/tests/tags.yml b/modules/nf-core/annotsv/installannotations/tests/tags.yml
deleted file mode 100644
index 232bec39..00000000
--- a/modules/nf-core/annotsv/installannotations/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-annotsv/installannotations:
-  - "modules/nf-core/annotsv/installannotations/**"
diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml
new file mode 100644
index 00000000..b562b72c
--- /dev/null
+++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  - bioconda::gcnvkernel=0.9
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
new file mode 100644
index 00000000..998622a0
--- /dev/null
+++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf
@@ -0,0 +1,52 @@
+process GATK4_CREATESEQUENCEDICTIONARY {
+    tag "$fasta"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
+        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path('*.dict')  , emit: dict
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    def avail_mem = 6144
+    if (!task.memory) {
+        log.info '[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
+        CreateSequenceDictionary \\
+        --REFERENCE $fasta \\
+        --URI $fasta \\
+        --TMP_DIR . \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${fasta.baseName}.dict
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml
new file mode 100644
index 00000000..72dced28
--- /dev/null
+++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml
@@ -0,0 +1,54 @@
+name: gatk4_createsequencedictionary
+description: Creates a sequence dictionary for a reference sequence
+keywords:
+  - createsequencedictionary
+  - dictionary
+  - fasta
+  - gatk4
+tools:
+  - gatk:
+      description: |
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      doi: 10.1158/1538-7445.AM2017-3590
+      licence: ["Apache-2.0"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Input fasta file
+        pattern: "*.{fasta,fa}"
+        ontologies: []
+output:
+  dict:
+    - - meta:
+          type: file
+          description: gatk dictionary file
+          pattern: "*.{dict}"
+          ontologies: []
+      - "*.dict":
+          type: file
+          description: gatk dictionary file
+          pattern: "*.{dict}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@maxulysse"
+  - "@ramprasadn"
+maintainers:
+  - "@maxulysse"
+  - "@ramprasadn"
diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test
new file mode 100644
index 00000000..a8a9c6d2
--- /dev/null
+++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test
@@ -0,0 +1,56 @@
+nextflow_process {
+
+    name "Test Process GATK4_CREATESEQUENCEDICTIONARY"
+    script "../main.nf"
+    process "GATK4_CREATESEQUENCEDICTIONARY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/createsequencedictionary"
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap
new file mode 100644
index 00000000..e8a600fd
--- /dev/null
+++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439"
+                ],
+                "dict": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T10:51:56.155954077"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.dict:md5,7362679f176e0f52add03c08f457f646"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439"
+                ],
+                "dict": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.dict:md5,7362679f176e0f52add03c08f457f646"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T10:51:45.562993875"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml
new file mode 100644
index 00000000..b562b72c
--- /dev/null
+++ b/modules/nf-core/gatk4/svannotate/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/gatk4
+  - bioconda::gatk4=4.6.1.0
+  - bioconda::gcnvkernel=0.9
diff --git a/modules/nf-core/gatk4/svannotate/main.nf b/modules/nf-core/gatk4/svannotate/main.nf
new file mode 100644
index 00000000..5d6f4fed
--- /dev/null
+++ b/modules/nf-core/gatk4/svannotate/main.nf
@@ -0,0 +1,70 @@
+process GATK4_SVANNOTATE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data':
+        'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi), path(bed), path(non_coding_bed)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fasta_fai)
+    tuple val(meta4), path(dict)
+    tuple val(meta5), path(gtf)
+
+    output:
+    tuple val(meta), path("*.vcf.gz")       , emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi")   , emit: tbi
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def intervals = bed ? "--intervals ${bed}" : ""
+    def reference = fasta ? "--reference ${fasta}" : ""
+    def transcripts = gtf ? "--protein-coding-gtf ${gtf}" : ""
+    def non_coding = non_coding_bed ? "--non-coding-bed ${non_coding_bed}" : ""
+
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[GATK SVAnnotate] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\
+        SVAnnotate \\
+        --variant ${vcf} \\
+        --output ${prefix}.vcf.gz \\
+        ${intervals} \\
+        ${reference} \\
+        ${transcripts} \\
+        ${non_coding} \\
+        --tmp-dir . \\
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo | gzip > ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gatk4/svannotate/meta.yml b/modules/nf-core/gatk4/svannotate/meta.yml
new file mode 100644
index 00000000..5e830c38
--- /dev/null
+++ b/modules/nf-core/gatk4/svannotate/meta.yml
@@ -0,0 +1,125 @@
+name: "gatk4_svannotate"
+description: Adds predicted functional consequence, gene overlap, and noncoding
+  element overlap annotations to SV VCF from GATK-SV pipeline. Input files are
+  an SV VCF, a GTF file containing primary or canonical transcripts, and a BED
+  file containing noncoding elements. Output file is an annotated SV VCF.
+keywords:
+  - annotate
+  - gatk4
+  - structural variants
+  - svannotate
+  - vcf
+tools:
+  - gatk4:
+      description: Genome Analysis Toolkit (GATK4)
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: "10.1158/1538-7445.AM2017-3590"
+      licence: ["BSD-3-clause"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: A VCF file created with a structural variant caller
+        pattern: "*.vcf.gz"
+        ontologies:
+          - edam: http://edamontology.org/format_3989 # GZIP format
+    - tbi:
+        type: file
+        description: The index file of the VCF
+        pattern: "*.vcf.gz.tbi"
+        ontologies: []
+    - bed:
+        type: file
+        description: Regions to limit the analysis to
+        pattern: "*.bed"
+        ontologies: []
+    - non_coding_bed:
+        type: file
+        description: File containing noncoding regions
+        pattern: "*.bed"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing FASTA information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Optional - reference FASTA file needed when the input is a
+          CRAM file
+        pattern: "*.{fasta,fa}"
+        ontologies: []
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing FAI information
+          e.g. [ id:'test', single_end:false ]
+    - fasta_fai:
+        type: file
+        description: Optional - index of the reference FASTA file needed when the
+          input is a CRAM file
+        pattern: "*.fai"
+        ontologies: []
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing DICT information
+          e.g. [ id:'test', single_end:false ]
+    - dict:
+        type: file
+        description: Optional - sequence dictionary of the reference FASTA file
+          needed when the input is a CRAM file
+        pattern: "*.dict"
+        ontologies: []
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing GTF information
+          e.g. [ id:'test', single_end:false ]
+    - gtf:
+        type: file
+        description: Optional - GTF file containing transcript information
+        pattern: "*.gtf"
+        ontologies: []
+output:
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.vcf.gz":
+          type: file
+          description: The annotated structural variant VCF
+          pattern: "*.vcf.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  tbi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.vcf.gz.tbi":
+          type: file
+          description: The index of the VCF
+          pattern: "*.vcf.gz.tbi"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/gatk4/svannotate/tests/main.nf.test b/modules/nf-core/gatk4/svannotate/tests/main.nf.test
new file mode 100644
index 00000000..1fd9b260
--- /dev/null
+++ b/modules/nf-core/gatk4/svannotate/tests/main.nf.test
@@ -0,0 +1,112 @@
+nextflow_process {
+
+    name "Test Process GATK4_SVANNOTATE"
+    script "../main.nf"
+    process "GATK4_SVANNOTATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "manta"
+    tag "manta/germline"
+    tag "gatk4"
+    tag "gatk4/svannotate"
+
+    setup {
+        run("MANTA_GERMLINE") {
+            script "../../../manta/germline/main.nf"
+            process {
+                """
+                input[0] = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], []])
+                input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)])
+                input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)])
+                input[3] = []
+                """
+            }
+        }
+    }
+
+    test("homo sapiens - defaults") {
+
+        when {
+            process {
+                """
+                input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.join(MANTA_GERMLINE.out.diploid_sv_vcf_tbi).map({ meta, vcf, tbi -> [ meta, vcf, tbi, [], [] ]})
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                input[3] = [[:],[]]
+                input[4] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { meta, vcf -> [ meta, file(vcf.toString()).name]},
+                    process.out.tbi.collect { meta, tbi -> [ meta, file(tbi.toString()).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+
+    test("homo sapiens - all") {
+
+        when {
+            process {
+                """
+                input[0] = MANTA_GERMLINE.out.diploid_sv_vcf
+                    .join(MANTA_GERMLINE.out.diploid_sv_vcf_tbi)
+                    .map { meta, vcf, tbi -> [
+                        meta,
+                        vcf,
+                        tbi,
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed'),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed'),
+                    ] }
+                input[1] = [[id:'fasta'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id:'fai'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[id:'dict'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]
+                input[4] = [[id:'gtf'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_minimal.gtf', checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf.collect { meta, vcf -> [ meta, file(vcf.toString()).name]},
+                    process.out.tbi.collect { meta, tbi -> [ meta, file(tbi.toString()).name] },
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo sapiens - defaults - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = MANTA_GERMLINE.out.diploid_sv_vcf.join(MANTA_GERMLINE.out.diploid_sv_vcf_tbi).map({ meta, vcf, tbi -> [ meta, vcf, tbi, [], [] ]})
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                input[3] = [[:],[]]
+                input[4] = [[:],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap b/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap
new file mode 100644
index 00000000..020125a7
--- /dev/null
+++ b/modules/nf-core/gatk4/svannotate/tests/main.nf.test.snap
@@ -0,0 +1,107 @@
+{
+    "homo sapiens - all": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi"
+                ]
+            ],
+            [
+                "versions.yml:md5,2969ab236c7c7c187097a1d5f2a109e3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-07-14T16:21:20.730000686"
+    },
+    "homo sapiens - defaults": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.vcf.gz.tbi"
+                ]
+            ],
+            [
+                "versions.yml:md5,2969ab236c7c7c187097a1d5f2a109e3"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-07-14T16:20:55.802118653"
+    },
+    "homo sapiens - defaults - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,2969ab236c7c7c187097a1d5f2a109e3"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2969ab236c7c7c187097a1d5f2a109e3"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-07-14T16:14:58.100341593"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/svync/environment.yml b/modules/nf-core/svync/environment.yml
index cada6309..b70ebfbf 100644
--- a/modules/nf-core/svync/environment.yml
+++ b/modules/nf-core/svync/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::svync=0.1.2
+  - bioconda::svync=0.3.0
diff --git a/modules/nf-core/svync/main.nf b/modules/nf-core/svync/main.nf
index 299229c6..18dbd918 100644
--- a/modules/nf-core/svync/main.nf
+++ b/modules/nf-core/svync/main.nf
@@ -4,8 +4,8 @@ process SVYNC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svync:0.1.2--h9ee0642_0':
-        'biocontainers/svync:0.1.2--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/svync:0.3.0--h9ee0642_0':
+        'biocontainers/svync:0.3.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(config)
diff --git a/modules/nf-core/svync/meta.yml b/modules/nf-core/svync/meta.yml
index 8da1fc49..2357aa15 100644
--- a/modules/nf-core/svync/meta.yml
+++ b/modules/nf-core/svync/meta.yml
@@ -25,17 +25,21 @@ input:
         type: file
         description: The input VCF file containing structural variants
         pattern: "*.{vcf,vcf.gz}"
+        ontologies: []
     - tbi:
         type: file
         description: The index of the input VCF file containing structural variants
         pattern: "*.tbi"
+        ontologies: []
     - config:
         type: file
         description: The config stating how the standardization should happen
         pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 output:
-  - vcf:
-      - meta:
+  vcf:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -44,8 +48,10 @@ output:
           type: file
           description: The standardized VCF file
           pattern: "*.vcf.gz"
-  - tbi:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  tbi:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -54,11 +60,14 @@ output:
           type: file
           description: The index of the standardized VCF file
           pattern: "*.tbi"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@nvnieuwk"
 maintainers:
diff --git a/modules/nf-core/svync/tests/main.nf.test.snap b/modules/nf-core/svync/tests/main.nf.test.snap
index f242ce9a..b4715e8e 100644
--- a/modules/nf-core/svync/tests/main.nf.test.snap
+++ b/modules/nf-core/svync/tests/main.nf.test.snap
@@ -21,15 +21,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,dd982c7896f22ebaa0ea51d00472c96c"
+                    "versions.yml:md5,37174a343ebe85fcce767948b2d3686e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-13T15:20:25.459243101"
+        "timestamp": "2025-07-16T13:46:13.393014929"
     },
     "sarscov2 - vcf, config - stub": {
         "content": [
@@ -53,14 +53,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,dd982c7896f22ebaa0ea51d00472c96c"
+                    "versions.yml:md5,37174a343ebe85fcce767948b2d3686e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-13T15:18:08.523826702"
+        "timestamp": "2025-07-16T13:46:22.727686645"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/svync/tests/tags.yml b/modules/nf-core/svync/tests/tags.yml
deleted file mode 100644
index e63467dc..00000000
--- a/modules/nf-core/svync/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-svync:
-  - "modules/nf-core/svync/**"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index bab849c9..deb02016 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -73,6 +73,22 @@
                     "pattern": "^\\S+\\.fai$",
                     "mimetype": "text/plain"
                 },
+                "dict": {
+                    "type": "string",
+                    "description": "The sequence dictionary of the FASTA reference file",
+                    "exists": true,
+                    "format": "file-path",
+                    "pattern": "^\\S+\\.dict$",
+                    "mimetype": "text/plain"
+                },
+                "gtf": {
+                    "type": "string",
+                    "description": "Path to GTF file for the reference genome. Gene and transcript annotations will be added when this file is provided",
+                    "exists": true,
+                    "format": "file-path",
+                    "pattern": "^\\S+\\.gtf$",
+                    "mimetype": "text/plain"
+                },
                 "expansionhunter_catalog": {
                     "type": "string",
                     "description": "Path to the expansionhunter catalog",
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 332cfa01..2751dfd5 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -18,6 +18,8 @@ params {
     // References for test data
     fasta                   = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.fasta"
     fai                     = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.fasta.fai"
+    dict                    = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.dict"
+    gtf                     = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/reference.gtf"
     bwa                     = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/seq/SVcontrol/bwa.tar.gz"
     expansionhunter_catalog = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/expansionhunter/variant_catalog.json"
     qdnaseq_male            = "https://github.com/nf-cmgg/test-datasets/raw/main/data/genomics/homo_sapiens/genome/qdnaseq/chr21.10kbp.rda"
diff --git a/tests/pipeline/all_types/all.nf.test.snap b/tests/pipeline/all_types/all.nf.test.snap
index e8904933..e7159c5e 100644
--- a/tests/pipeline/all_types/all.nf.test.snap
+++ b/tests/pipeline/all_types/all.nf.test.snap
@@ -2,7 +2,7 @@
     "all": {
         "content": [
             [
-                
+
             ],
             [
                 "PosCon1/PosCon1.cnv.vcf.gz",
@@ -82,7 +82,7 @@
     "concat": {
         "content": [
             [
-                
+
             ],
             [
                 "PosCon1/PosCon1.vcf.gz",
@@ -141,12 +141,12 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-07-10T16:20:18.015157817"
+        "timestamp": "2025-07-22T11:45:55.747550179"
     },
     "output callers": {
         "content": [
             [
-                
+
             ],
             [
                 "PosCon1/PosCon1.cnv.vcf.gz",
@@ -255,4 +255,4 @@
         },
         "timestamp": "2025-07-10T16:21:41.411733092"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/subworkflows/local/bam_sv_calling/main.nf.test.snap b/tests/subworkflows/local/bam_sv_calling/main.nf.test.snap
index 1373c202..eece493f 100644
--- a/tests/subworkflows/local/bam_sv_calling/main.nf.test.snap
+++ b/tests/subworkflows/local/bam_sv_calling/main.nf.test.snap
@@ -15,7 +15,7 @@
                     ]
                 ],
                 "reports": [
-                    
+
                 ],
                 "vcfs": [
                     [
@@ -53,7 +53,7 @@
                     ]
                 ],
                 "reports": [
-                    
+
                 ],
                 "vcfs": [
                     [
@@ -63,17 +63,17 @@
                             "sex": "male",
                             "variant_type": "sv"
                         },
-                        "test.svync.manta.vcf.gz,variantsMD5:73d9618ba3a50341575d3c9c1d2796ab",
+                        "test.svync.manta.vcf.gz,variantsMD5:a25dede957f135ec2f76266f06cac512",
                         "test.svync.manta.vcf.gz.tbi"
                     ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-13T17:25:48.450406346"
+        "timestamp": "2025-07-22T12:13:19.296439771"
     },
     "homo_sapiens - delly": {
         "content": [
@@ -91,7 +91,7 @@
                     ]
                 ],
                 "reports": [
-                    
+
                 ],
                 "vcfs": [
                     [
@@ -101,17 +101,17 @@
                             "sex": "male",
                             "variant_type": "sv"
                         },
-                        "test.svync.delly.vcf.gz,variantsMD5:caf4116f675c20783b0119c98e70f2ea",
+                        "test.svync.delly.vcf.gz,variantsMD5:e15d4c5f477f8e86b4d077da42b9de83",
                         "test.svync.delly.vcf.gz.tbi"
                     ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-13T17:26:06.285138049"
+        "timestamp": "2025-07-22T12:14:02.716091083"
     },
     "homo_sapiens - all sv callers": {
         "content": [
@@ -149,7 +149,7 @@
                     ]
                 ],
                 "reports": [
-                    
+
                 ],
                 "vcfs": [
                     [
@@ -159,16 +159,16 @@
                             "sex": "male",
                             "variant_type": "sv"
                         },
-                        "test.sv.vcf.gz,variantsMD5:2d626bce1f675bc7c41ec59d9a09a7aa",
+                        "test.sv.vcf.gz,variantsMD5:fb4b0ff0cd5dcb247c0fe1fbcb246cc5",
                         "test.sv.vcf.gz.tbi"
                     ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-13T17:26:51.327526373"
+        "timestamp": "2025-07-22T12:15:39.713604515"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/subworkflows/local/bam_variant_calling_delly/main.nf.test.snap b/tests/subworkflows/local/bam_variant_calling_delly/main.nf.test.snap
index 70dcc22a..140a46e3 100644
--- a/tests/subworkflows/local/bam_variant_calling_delly/main.nf.test.snap
+++ b/tests/subworkflows/local/bam_variant_calling_delly/main.nf.test.snap
@@ -10,7 +10,7 @@
                             "sex": "male",
                             "caller": "delly"
                         },
-                        "test.svync.delly.vcf.gz,variantsMD5:caf4116f675c20783b0119c98e70f2ea",
+                        "test.svync.delly.vcf.gz,variantsMD5:e15d4c5f477f8e86b4d077da42b9de83",
                         "test.svync.delly.vcf.gz.tbi"
                     ]
                 ],
@@ -29,9 +29,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-02-13T16:40:54.037387408"
+        "timestamp": "2025-07-22T12:16:17.594443126"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/subworkflows/local/bam_variant_calling_manta/main.nf.test.snap b/tests/subworkflows/local/bam_variant_calling_manta/main.nf.test.snap
index 29e4a231..879236d5 100644
--- a/tests/subworkflows/local/bam_variant_calling_manta/main.nf.test.snap
+++ b/tests/subworkflows/local/bam_variant_calling_manta/main.nf.test.snap
@@ -5,16 +5,16 @@
                 "##contig=<ID=chr16,length=2000001>",
                 "##contig=<ID=chrX,length=2000001>",
                 "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tPosCon1",
-                "chr16\t1061455\tmanta_DEL_1\tGTTCCACTCATGTTGTTGCAGATTACTGGATCTCACTCTTTTTTATGGGTGAATCGTACTTCATAGTGTATATGTACC\tG\t619\tPASS\tCALLERS=manta;CIPOS=0,5;END=1061532;SVLEN=-77;SVTYPE=DEL\tGT:PE:SR\t1/1:0,0:0,19"
+                "chr16\t1061455\tmanta_DEL_1\tGTTCCACTCATGTTGTTGCAGATTACTGGATCTCACTCTTTTTTATGGGTGAATCGTACTTCATAGTGTATATGTACC\t<DEL>\t619\tPASS\tCALLERS=manta;CIPOS=0,5;END=1061532;SVLEN=-77;SVTYPE=DEL\tGT:PE:SR\t1/1:0,0:0,19"
             ],
             "test.svync.manta.vcf.gz.tbi",
             6,
             0
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-03-11T14:12:51.499950856"
+        "timestamp": "2025-07-22T12:16:57.486074419"
     }
-}
\ No newline at end of file
+}
diff --git a/workflows/structural.nf b/workflows/structural.nf
index c899bd54..66527af1 100644
--- a/workflows/structural.nf
+++ b/workflows/structural.nf
@@ -37,6 +37,8 @@ include { VCF_MERGE_FAMILY_JASMINE              } from '../subworkflows/local/vc
 // MODULE: Installed directly from nf-core/modules
 //
 include { SAMTOOLS_FAIDX                    } from '../modules/nf-core/samtools/faidx/main'
+include { GATK4_CREATESEQUENCEDICTIONARY    } from '../modules/nf-core/gatk4/createsequencedictionary/main'
+include { PREPROCESS_GTF                    } from '../modules/local/preprocess_gtf/main'
 include { BWA_INDEX                         } from '../modules/nf-core/bwa/index/main'
 include { ENSEMBLVEP_DOWNLOAD               } from '../modules/nf-core/ensemblvep/download/main'
 include { ANNOTSV_INSTALLANNOTATIONS        } from '../modules/nf-core/annotsv/installannotations/main'
@@ -45,6 +47,7 @@ include { UNTAR as UNTAR_BWA                } from '../modules/nf-core/untar/mai
 include { NGSBITS_SAMPLEGENDER              } from '../modules/nf-core/ngsbits/samplegender/main'
 include { BCFTOOLS_FILTER                   } from '../modules/nf-core/bcftools/filter/main'
 include { SVTOOLS_VCFTOBEDPE                } from '../modules/nf-core/svtools/vcftobedpe/main'
+include { GATK4_SVANNOTATE                  } from '../modules/nf-core/gatk4/svannotate/main'
 include { MULTIQC                           } from '../modules/nf-core/multiqc/main'
 
 /*
@@ -66,6 +69,8 @@ workflow STRUCTURAL {
     // file inputs
     fasta                       // The fasta file to use
     fai                         // The index of the fasta file
+    dict                        // The dictionary of the fasta file
+    gtf                         // The GTF file to use for annotation
     expansionhunter_catalog     // The expansionhunter catalog
     qdnaseq_female              // The QDNAseq annotations for female samples
     qdnaseq_male                // The QDNAseq annotations for male samples
@@ -200,6 +205,32 @@ workflow STRUCTURAL {
         ch_fai = Channel.fromPath(fai).collect { fai_file -> [[id:'fai'], fai_file] }
     }
 
+    def ch_dict = Channel.empty()
+    // Dictionary is only needed for GATK4_SVANNOTATE
+    if(!dict && gtf) {
+        GATK4_CREATESEQUENCEDICTIONARY(
+            ch_fasta
+        )
+        ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions)
+
+        ch_dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict.collect()
+    }
+    else if(dict) {
+        ch_dict = Channel.fromPath(dict).collect { dict_file -> [[id:'dict'], dict_file] }
+    }
+
+    def ch_preprocessed_gtf = Channel.empty()
+    // Sanitize GTF file to adhere to the extremely strict GTF parsing in SVAnnotate
+    if (gtf) {
+        ch_sanitize_input = Channel.fromPath(gtf).collect { gtf_file -> [[id:'gtf'], gtf_file] }
+        PREPROCESS_GTF(
+            ch_sanitize_input
+        )
+        ch_versions = ch_versions.mix(PREPROCESS_GTF.out.versions)
+
+        ch_preprocessed_gtf = PREPROCESS_GTF.out.gtf.collect()
+    }
+
     // if(!bwa && "gridss" in callers){
     //     BWA_INDEX(
     //         ch_fasta
@@ -427,16 +458,35 @@ workflow STRUCTURAL {
         ch_vcfanno_output  = ch_annotation_input
     }
 
-    def ch_outputs = Channel.empty()
+    def ch_filter_outputs = Channel.empty()
     if(filter) {
         BCFTOOLS_FILTER(
             ch_vcfanno_output
         )
-        def ch_filter_output = BCFTOOLS_FILTER.out.vcf.join(BCFTOOLS_FILTER.out.tbi, failOnMismatch:true, failOnDuplicate:true)
-        ch_outputs = ch_outputs.mix(ch_filter_output)
+        ch_filter_outputs = BCFTOOLS_FILTER.out.vcf.join(BCFTOOLS_FILTER.out.tbi, failOnMismatch:true, failOnDuplicate:true)
         ch_versions = ch_versions.mix(BCFTOOLS_FILTER.out.versions)
     } else {
-        ch_outputs = ch_outputs.mix(ch_vcfanno_output)
+        ch_filter_outputs = ch_vcfanno_output
+    }
+
+    def ch_outputs = Channel.empty()
+    if(gtf) {
+        def ch_svannotate_input = ch_filter_outputs
+            .map { meta, vcf, tbi ->
+                [ meta, vcf, tbi, [], [] ] // TODO add BED files
+            }
+
+        GATK4_SVANNOTATE(
+            ch_svannotate_input,
+            ch_fasta,
+            ch_fai,
+            ch_dict,
+            ch_preprocessed_gtf
+        )
+        ch_versions = ch_versions.mix(GATK4_SVANNOTATE.out.versions.first())
+        ch_outputs = ch_outputs.mix(GATK4_SVANNOTATE.out.vcf.join(GATK4_SVANNOTATE.out.tbi, failOnMismatch:true, failOnDuplicate:true))
+    } else {
+        ch_outputs = ch_outputs.mix(ch_filter_outputs)
     }
 
     //