diff --git a/snappy_pipeline/workflows/common/gcnv/gcnv_run.py b/snappy_pipeline/workflows/common/gcnv/gcnv_run.py
index 3fffb9c3b..1388a2c67 100644
--- a/snappy_pipeline/workflows/common/gcnv/gcnv_run.py
+++ b/snappy_pipeline/workflows/common/gcnv/gcnv_run.py
@@ -516,7 +516,7 @@ def get_result_files(self):
 
         The function will skip pedigrees where samples have inconsistent library kits and print a warning.
         """
-        if "gcnv" not in self.config["tools"]:
+        if "gcnv" not in self.config["tools"] and "gcnv" not in self.config["tools"].get("dna", {}):
             return
 
         # Get list with all result path template strings.
diff --git a/snappy_pipeline/workflows/common/sv_calling.py b/snappy_pipeline/workflows/common/sv_calling.py
index 0e045f1cb..3fd6183c9 100644
--- a/snappy_pipeline/workflows/common/sv_calling.py
+++ b/snappy_pipeline/workflows/common/sv_calling.py
@@ -17,7 +17,9 @@ def get_result_files(self):
         The implementation will return a list of all paths with prefix ``output/` that are
         returned by ``self.get_output_files()`` for all actions in ``self.actions``.
         """
-        if self.name not in self.config["tools"]:
+        if self.name not in self.config["tools"] and not (
+            hasattr(self.config, "tools") and self.name in self.config["tools"].get("dna", {})
+        ):
             return  # tool not enabled, no result files
 
         ngs_mapping_config = DictQuery(self.w_config).get("step_config/ngs_mapping")
diff --git a/snappy_pipeline/workflows/sv_calling_wgs/Snakefile b/snappy_pipeline/workflows/sv_calling_wgs/Snakefile
index fca344e55..af67ca8a4 100644
--- a/snappy_pipeline/workflows/sv_calling_wgs/Snakefile
+++ b/snappy_pipeline/workflows/sv_calling_wgs/Snakefile
@@ -4,7 +4,7 @@
 import os
 
 from snappy_pipeline import expand_ref
-from snappy_pipeline.workflows.sv_calling_wgs import WgsSvCallingWorkflow
+from snappy_pipeline.workflows.sv_calling_wgs import SvCallingWgsWorkflow
 
 __author__ = "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>"
 
@@ -20,15 +20,11 @@ config, lookup_paths, config_paths = expand_ref("config.yaml", config)
 
 # WorkflowImpl Object Setup ===================================================
 
-wf = WgsSvCallingWorkflow(workflow, config, lookup_paths, config_paths, os.getcwd())
+wf = SvCallingWgsWorkflow(workflow, config, lookup_paths, config_paths, os.getcwd())
 
 # Rules =======================================================================
 
 
-localrules:
-    sv_calling_wgs_write_pedigree,
-
-
 rule all:
     input:
         wf.get_result_files(),
@@ -39,7 +35,7 @@ rule all:
 # Write out pedigree file -----------------------------------------------------
 
 
-rule sv_calling_targeted_write_pedigree_run:
+rule sv_calling_wgs_write_pedigree_run:
     output:
         wf.get_output_files("write_pedigree", "run"),
     run:
@@ -53,7 +49,7 @@ rule sv_calling_targeted_write_pedigree_run:
 
 rule sv_calling_wgs_manta_run:
     input:
-        wf.get_input_files("manta", "run"),
+        unpack(wf.get_input_files("manta", "run")),
     output:
         **wf.get_output_files("manta", "run"),
     threads: wf.get_resource("manta", "run", "threads")
@@ -63,7 +59,7 @@ rule sv_calling_wgs_manta_run:
         partition=wf.get_resource("manta", "run", "partition"),
         tmpdir=wf.get_resource("manta", "run", "tmpdir"),
     log:
-        wf.get_log_file("manta", "run"),
+        **wf.get_log_file("manta", "run"),
     wrapper:
         wf.wrapper_path("manta/germline_wgs")
 
@@ -84,16 +80,15 @@ rule sv_calling_wgs_delly2_call:
         tmpdir=wf.get_resource("delly2", "call", "tmpdir"),
     params:
         step_key="sv_calling_wgs",
-        library_info=wf.substep_getattr("delly2", "get_library_extra_infos"),
     log:
-        wf.get_log_file("delly2", "call"),
+        **wf.get_log_file("delly2", "call"),
     wrapper:
         wf.wrapper_path("delly2/germline/call")
 
 
 rule sv_calling_wgs_delly2_merge_calls:
     input:
-        wf.get_input_files("delly2", "merge_calls"),
+        unpack(wf.get_input_files("delly2", "merge_calls")),
     output:
         **wf.get_output_files("delly2", "merge_calls"),
     threads: wf.get_resource("delly2", "merge_calls", "threads")
@@ -105,7 +100,7 @@ rule sv_calling_wgs_delly2_merge_calls:
     params:
         step_key="sv_calling_wgs",
     log:
-        wf.get_log_file("delly2", "merge_calls"),
+        **wf.get_log_file("delly2", "merge_calls"),
     wrapper:
         wf.wrapper_path("delly2/germline/merge_calls")
 
@@ -123,16 +118,15 @@ rule sv_calling_wgs_delly2_genotype:
         tmpdir=wf.get_resource("delly2", "genotype", "tmpdir"),
     params:
         step_key="sv_calling_wgs",
-        library_info=wf.substep_getattr("delly2", "get_library_extra_infos"),
     log:
-        wf.get_log_file("delly2", "genotype"),
+        **wf.get_log_file("delly2", "genotype"),
     wrapper:
         wf.wrapper_path("delly2/germline/genotype")
 
 
 rule sv_calling_wgs_delly2_merge_genotypes:
     input:
-        wf.get_input_files("delly2", "merge_genotypes"),
+        unpack(wf.get_input_files("delly2", "merge_genotypes")),
     output:
         **wf.get_output_files("delly2", "merge_genotypes"),
     threads: wf.get_resource("delly2", "merge_genotypes", "threads")
@@ -144,163 +138,391 @@ rule sv_calling_wgs_delly2_merge_genotypes:
     params:
         step_key="sv_calling_wgs",
     log:
-        wf.get_log_file("delly2", "merge_genotypes"),
+        **wf.get_log_file("delly2", "merge_genotypes"),
     wrapper:
         wf.wrapper_path("delly2/germline/merge_genotypes")
 
 
-# Run PB Honey Spots ----------------------------------------------------------
-
-
-rule sv_calling_wgs_pb_honey_spots_run:
+## Run Sniffles ----------------------------------------------------------------
+#
+#
+# rule sv_calling_wgs_sniffles_run:
+#    input:
+#        wf.get_input_files("sniffles", "run"),
+#    output:
+#        **wf.get_output_files("sniffles", "run"),
+#    threads: wf.get_resource("sniffles", "run", "threads")
+#    resources:
+#        time=wf.get_resource("sniffles", "run", "time"),
+#        memory=wf.get_resource("sniffles", "run", "memory"),
+#        partition=wf.get_resource("sniffles", "run", "partition"),
+#        tmpdir=wf.get_resource("sniffles", "run", "tmpdir"),
+#    log:
+#        wf.get_log_file("sniffles", "run"),
+#    wrapper:
+#        wf.wrapper_path("sniffles/germline")
+#
+#
+## Run Sniffles 2 --------------------------------------------------------------
+#
+#
+# rule sv_calling_wgs_sniffles2_bam_to_snf:
+#    input:
+#        unpack(wf.get_input_files("sniffles2", "bam_to_snf")),
+#    output:
+#        **wf.get_output_files("sniffles2", "bam_to_snf"),
+#    threads: wf.get_resource("sniffles2", "bam_to_snf", "threads")
+#    resources:
+#        time=wf.get_resource("sniffles2", "bam_to_snf", "time"),
+#        memory=wf.get_resource("sniffles2", "bam_to_snf", "memory"),
+#        partition=wf.get_resource("sniffles2", "bam_to_snf", "partition"),
+#        tmpdir=wf.get_resource("sniffles2", "bam_to_snf", "tmpdir"),
+#    log:
+#        wf.get_log_file("sniffles2", "bam_to_snf"),
+#    wrapper:
+#        wf.wrapper_path("sniffles2/germline/bam_to_snf")
+#
+#
+# rule sv_calling_wgs_sniffles2_snf_to_vcf:
+#    input:
+#        unpack(wf.get_input_files("sniffles2", "snf_to_vcf")),
+#    output:
+#        **wf.get_output_files("sniffles2", "snf_to_vcf"),
+#    threads: wf.get_resource("sniffles2", "snf_to_vcf", "threads")
+#    resources:
+#        time=wf.get_resource("sniffles2", "snf_to_vcf", "time"),
+#        memory=wf.get_resource("sniffles2", "snf_to_vcf", "memory"),
+#        partition=wf.get_resource("sniffles2", "snf_to_vcf", "partition"),
+#        tmpdir=wf.get_resource("sniffles2", "snf_to_vcf", "tmpdir"),
+#    log:
+#        wf.get_log_file("sniffles2", "snf_to_vcf"),
+#    wrapper:
+#        wf.wrapper_path("sniffles2/germline/snf_to_vcf")
+
+
+## PopDel Steps ----------------------------------------------------------------
+#
+#
+# ruleorder: sv_calling_wgs_popdel_reorder_vcf > sv_calling_wgs_popdel_concat_calls > sv_calling_wgs_popdel_call > sv_calling_wgs_popdel_profile
+#
+#
+# rule sv_calling_wgs_popdel_profile:
+#    input:
+#        unpack(wf.get_input_files("popdel", "profile")),
+#    output:
+#        **wf.get_output_files("popdel", "profile"),
+#    threads: wf.get_resource("popdel", "profile", "threads")
+#    resources:
+#        time=wf.get_resource("popdel", "profile", "time"),
+#        memory=wf.get_resource("popdel", "profile", "memory"),
+#        partition=wf.get_resource("popdel", "profile", "partition"),
+#        tmpdir=wf.get_resource("popdel", "profile", "tmpdir"),
+#    wildcard_constraints:
+#        index_ngs_library=r"[^\.]+",
+#    log:
+#        **wf.get_log_file("popdel", "profile"),
+#    wrapper:
+#        wf.wrapper_path("popdel/profile")
+#
+#
+# rule sv_calling_wgs_popdel_call:
+#    input:
+#        unpack(wf.get_input_files("popdel", "call")),
+#    output:
+#        **wf.get_output_files("popdel", "call"),
+#    threads: wf.get_resource("popdel", "call", "threads")
+#    resources:
+#        time=wf.get_resource("popdel", "call", "time"),
+#        memory=wf.get_resource("popdel", "call", "memory"),
+#        partition=wf.get_resource("popdel", "call", "partition"),
+#        tmpdir=wf.get_resource("popdel", "call", "tmpdir"),
+#    log:
+#        **wf.get_log_file("popdel", "call"),
+#    wrapper:
+#        wf.wrapper_path("popdel/call")
+#
+#
+# rule sv_calling_wgs_popdel_concat_calls:
+#    input:
+#        unpack(wf.get_input_files("popdel", "concat_calls")),
+#    output:
+#        **wf.get_output_files("popdel", "concat_calls"),
+#    threads: wf.get_resource("popdel", "concat_calls", "threads")
+#    resources:
+#        time=wf.get_resource("popdel", "concat_calls", "time"),
+#        memory=wf.get_resource("popdel", "concat_calls", "memory"),
+#        partition=wf.get_resource("popdel", "concat_calls", "partition"),
+#        tmpdir=wf.get_resource("popdel", "concat_calls", "tmpdir"),
+#    log:
+#        **wf.get_log_file("popdel", "concat_calls"),
+#    wrapper:
+#        wf.wrapper_path("popdel/concat_calls")
+#
+#
+# rule sv_calling_wgs_popdel_reorder_vcf:
+#    input:
+#        unpack(wf.get_input_files("popdel", "reorder_vcf")),
+#    output:
+#        **wf.get_output_files("popdel", "reorder_vcf"),
+#    threads: wf.get_resource("popdel", "reorder_vcf", "threads")
+#    resources:
+#        time=wf.get_resource("popdel", "reorder_vcf", "time"),
+#        memory=wf.get_resource("popdel", "reorder_vcf", "memory"),
+#        partition=wf.get_resource("popdel", "reorder_vcf", "partition"),
+#        tmpdir=wf.get_resource("popdel", "reorder_vcf", "tmpdir"),
+#    wildcard_constraints:
+#        index_ngs_library=r"[^\.]+",
+#    params:
+#        ped_members=wf.substep_getattr("popdel", "get_ped_members"),
+#    log:
+#        **wf.get_log_file("popdel", "reorder_vcf"),
+#    wrapper:
+#        wf.wrapper_path("popdel/reorder_vcf")
+
+
+# Run Melt --------------------------------------------------------------------
+
+
+# Regular expression for wildcard constraints
+RE_NO_DOT = r"[^.]+"
+
+
+rule sv_calling_wgs_melt_preprocess:
     input:
-        wf.get_input_files("pb_honey_spots", "run"),
+        unpack(wf.get_input_files("melt", "preprocess")),
     output:
-        **wf.get_output_files("pb_honey_spots", "run"),
-    threads: wf.get_resource("pb_honey_spots", "run", "threads")
+        **wf.get_output_files("melt", "preprocess"),
+    wildcard_constraints:
+        mapper=RE_NO_DOT,
+        library_name=RE_NO_DOT,
+        me_type=RE_NO_DOT,
+    threads: wf.get_resource("melt", "preprocess", "threads")
     resources:
-        time=wf.get_resource("pb_honey_spots", "run", "time"),
-        memory=wf.get_resource("pb_honey_spots", "run", "memory"),
-        partition=wf.get_resource("pb_honey_spots", "run", "partition"),
-        tmpdir=wf.get_resource("pb_honey_spots", "run", "tmpdir"),
+        time=wf.get_resource("melt", "preprocess", "time"),
+        memory=wf.get_resource("melt", "preprocess", "memory"),
+        partition=wf.get_resource("melt", "preprocess", "partition"),
     log:
-        wf.get_log_file("pb_honey_spots", "run"),
+        **wf.get_log_file("melt", "preprocess"),
+    params:
+        step_key="sv_calling_wgs",
     wrapper:
-        wf.wrapper_path("pb_honey_spots/germline")
+        wf.wrapper_path("melt/preprocess")
 
 
-# Run Sniffles ----------------------------------------------------------------
+rule sv_calling_wgs_melt_indiv_analysis:
+    input:
+        unpack(wf.get_input_files("melt", "indiv_analysis")),
+    output:
+        **wf.get_output_files("melt", "indiv_analysis"),
+    wildcard_constraints:
+        mapper=RE_NO_DOT,
+        library_name=RE_NO_DOT,
+        me_type=RE_NO_DOT,
+    threads: wf.get_resource("melt", "indiv_analysis", "threads")
+    resources:
+        time=wf.get_resource("melt", "indiv_analysis", "time"),
+        memory=wf.get_resource("melt", "indiv_analysis", "memory"),
+        partition=wf.get_resource("melt", "indiv_analysis", "partition"),
+    log:
+        **wf.get_log_file("melt", "indiv_analysis"),
+    params:
+        step_key="sv_calling_wgs",
+    wrapper:
+        wf.wrapper_path("melt/indiv_analysis")
 
 
-rule sv_calling_wgs_sniffles_run:
+rule sv_calling_wgs_melt_group_analysis:
     input:
-        wf.get_input_files("sniffles", "run"),
+        unpack(wf.get_input_files("melt", "group_analysis")),
     output:
-        **wf.get_output_files("sniffles", "run"),
-    threads: wf.get_resource("sniffles", "run", "threads")
+        **wf.get_output_files("melt", "group_analysis"),
+    wildcard_constraints:
+        mapper=RE_NO_DOT,
+        index_library_name=RE_NO_DOT,
+        me_type=RE_NO_DOT,
+    threads: wf.get_resource("melt", "group_analysis", "threads")
     resources:
-        time=wf.get_resource("sniffles", "run", "time"),
-        memory=wf.get_resource("sniffles", "run", "memory"),
-        partition=wf.get_resource("sniffles", "run", "partition"),
-        tmpdir=wf.get_resource("sniffles", "run", "tmpdir"),
+        time=wf.get_resource("melt", "group_analysis", "time"),
+        memory=wf.get_resource("melt", "group_analysis", "memory"),
+        partition=wf.get_resource("melt", "group_analysis", "partition"),
     log:
-        wf.get_log_file("sniffles", "run"),
+        **wf.get_log_file("melt", "group_analysis"),
+    params:
+        step_key="sv_calling_wgs",
     wrapper:
-        wf.wrapper_path("sniffles/germline")
+        wf.wrapper_path("melt/group_analysis")
 
 
-# Run Sniffles 2 --------------------------------------------------------------
+rule sv_calling_wgs_melt_genotype:
+    input:
+        unpack(wf.get_input_files("melt", "genotype")),
+    output:
+        **wf.get_output_files("melt", "genotype"),
+    wildcard_constraints:
+        mapper=RE_NO_DOT,
+        index_library_name=RE_NO_DOT,
+        me_type=RE_NO_DOT,
+    threads: wf.get_resource("melt", "genotype", "threads")
+    resources:
+        time=wf.get_resource("melt", "genotype", "time"),
+        memory=wf.get_resource("melt", "genotype", "memory"),
+        partition=wf.get_resource("melt", "genotype", "partition"),
+    log:
+        **wf.get_log_file("melt", "genotype"),
+    params:
+        step_key="sv_calling_wgs",
+    wrapper:
+        wf.wrapper_path("melt/genotype")
 
 
-rule sv_calling_wgs_sniffles2_bam_to_snf:
+rule sv_calling_wgs_melt_make_vcf:
     input:
-        unpack(wf.get_input_files("sniffles2", "bam_to_snf")),
+        unpack(wf.get_input_files("melt", "make_vcf")),
     output:
-        **wf.get_output_files("sniffles2", "bam_to_snf"),
-    threads: wf.get_resource("sniffles2", "bam_to_snf", "threads")
+        **wf.get_output_files("melt", "make_vcf"),
+    wildcard_constraints:
+        mapper=RE_NO_DOT,
+        index_library_name=RE_NO_DOT,
+    threads: wf.get_resource("melt", "make_vcf", "threads")
     resources:
-        time=wf.get_resource("sniffles2", "bam_to_snf", "time"),
-        memory=wf.get_resource("sniffles2", "bam_to_snf", "memory"),
-        partition=wf.get_resource("sniffles2", "bam_to_snf", "partition"),
-        tmpdir=wf.get_resource("sniffles2", "bam_to_snf", "tmpdir"),
+        time=wf.get_resource("melt", "make_vcf", "time"),
+        memory=wf.get_resource("melt", "make_vcf", "memory"),
+        partition=wf.get_resource("melt", "make_vcf", "partition"),
     log:
-        wf.get_log_file("sniffles2", "bam_to_snf"),
+        **wf.get_log_file("melt", "make_vcf"),
+    params:
+        step_key="sv_calling_wgs",
     wrapper:
-        wf.wrapper_path("sniffles2/germline/bam_to_snf")
+        wf.wrapper_path("melt/make_vcf")
 
 
-rule sv_calling_wgs_sniffles2_snf_to_vcf:
+rule sv_calling_wgs_melt_merge_vcf:
     input:
-        unpack(wf.get_input_files("sniffles2", "snf_to_vcf")),
+        unpack(wf.get_input_files("melt", "merge_vcf")),
     output:
-        **wf.get_output_files("sniffles2", "snf_to_vcf"),
-    threads: wf.get_resource("sniffles2", "snf_to_vcf", "threads")
+        **wf.get_output_files("melt", "merge_vcf"),
+    wildcard_constraints:
+        mapper=RE_NO_DOT,
+        library_name=RE_NO_DOT,
+    threads: wf.get_resource("melt", "merge_vcf", "threads")
     resources:
-        time=wf.get_resource("sniffles2", "snf_to_vcf", "time"),
-        memory=wf.get_resource("sniffles2", "snf_to_vcf", "memory"),
-        partition=wf.get_resource("sniffles2", "snf_to_vcf", "partition"),
-        tmpdir=wf.get_resource("sniffles2", "snf_to_vcf", "tmpdir"),
+        time=wf.get_resource("melt", "merge_vcf", "time"),
+        memory=wf.get_resource("melt", "merge_vcf", "memory"),
+        partition=wf.get_resource("melt", "merge_vcf", "partition"),
     log:
-        wf.get_log_file("sniffles2", "snf_to_vcf"),
+        **wf.get_log_file("melt", "merge_vcf"),
+    params:
+        step_key="sv_calling_wgs",
     wrapper:
-        wf.wrapper_path("sniffles2/germline/snf_to_vcf")
+        wf.wrapper_path("melt/merge_vcf")
 
 
-# PopDel Steps ----------------------------------------------------------------
+# GATK-gCNV -------------------------------------------------------------------
 
 
-ruleorder: sv_calling_wgs_popdel_reorder_vcf > sv_calling_wgs_popdel_concat_calls > sv_calling_wgs_popdel_call > sv_calling_wgs_popdel_profile
+rule sv_calling_wgs_gcnv_preprocess_intervals:
+    input:
+        unpack(wf.get_input_files("gcnv", "preprocess_intervals")),
+    output:
+        **wf.get_output_files("gcnv", "preprocess_intervals"),
+    threads: wf.get_resource("gcnv", "preprocess_intervals", "threads")
+    resources:
+        time=wf.get_resource("gcnv", "preprocess_intervals", "time"),
+        memory=wf.get_resource("gcnv", "preprocess_intervals", "memory"),
+        partition=wf.get_resource("gcnv", "preprocess_intervals", "partition"),
+        tmpdir=wf.get_resource("gcnv", "preprocess_intervals", "tmpdir"),
+    log:
+        wf.get_log_file("gcnv", "preprocess_intervals"),
+    wrapper:
+        wf.wrapper_path("gcnv/preprocess_intervals")
 
 
-rule sv_calling_wgs_popdel_profile:
+rule sv_calling_wgs_gcnv_coverage:
     input:
-        unpack(wf.get_input_files("popdel", "profile")),
+        unpack(wf.get_input_files("gcnv", "coverage")),
     output:
-        **wf.get_output_files("popdel", "profile"),
-    threads: wf.get_resource("popdel", "profile", "threads")
+        **wf.get_output_files("gcnv", "coverage"),
+    threads: wf.get_resource("gcnv", "coverage", "threads")
     resources:
-        time=wf.get_resource("popdel", "profile", "time"),
-        memory=wf.get_resource("popdel", "profile", "memory"),
-        partition=wf.get_resource("popdel", "profile", "partition"),
-        tmpdir=wf.get_resource("popdel", "profile", "tmpdir"),
-    wildcard_constraints:
-        index_ngs_library=r"[^\.]+",
+        time=wf.get_resource("gcnv", "coverage", "time"),
+        memory=wf.get_resource("gcnv", "coverage", "memory"),
+        partition=wf.get_resource("gcnv", "coverage", "partition"),
+        tmpdir=wf.get_resource("gcnv", "coverage", "tmpdir"),
     log:
-        **wf.get_log_file("popdel", "profile"),
+        wf.get_log_file("gcnv", "coverage"),
     wrapper:
-        wf.wrapper_path("popdel/profile")
+        wf.wrapper_path("gcnv/coverage")
 
 
-rule sv_calling_wgs_popdel_call:
+rule sv_calling_wgs_gcnv_contig_ploidy:
     input:
-        unpack(wf.get_input_files("popdel", "call")),
+        unpack(wf.get_input_files("gcnv", "contig_ploidy")),
     output:
-        **wf.get_output_files("popdel", "call"),
-    threads: wf.get_resource("popdel", "call", "threads")
+        **wf.get_output_files("gcnv", "contig_ploidy"),
+    threads: wf.get_resource("gcnv", "contig_ploidy", "threads")
     resources:
-        time=wf.get_resource("popdel", "call", "time"),
-        memory=wf.get_resource("popdel", "call", "memory"),
-        partition=wf.get_resource("popdel", "call", "partition"),
-        tmpdir=wf.get_resource("popdel", "call", "tmpdir"),
+        time=wf.get_resource("gcnv", "contig_ploidy", "time"),
+        memory=wf.get_resource("gcnv", "contig_ploidy", "memory"),
+        partition=wf.get_resource("gcnv", "contig_ploidy", "partition"),
+        tmpdir=wf.get_resource("gcnv", "contig_ploidy", "tmpdir"),
     log:
-        **wf.get_log_file("popdel", "call"),
+        wf.get_log_file("gcnv", "contig_ploidy"),
+    params:
+        args=wf.get_params("gcnv", "contig_ploidy"),
     wrapper:
-        wf.wrapper_path("popdel/call")
+        wf.wrapper_path("gcnv/contig_ploidy_case_mode")
 
 
-rule sv_calling_wgs_popdel_concat_calls:
+rule sv_calling_wgs_gcnv_call_cnvs:
     input:
-        unpack(wf.get_input_files("popdel", "concat_calls")),
+        unpack(wf.get_input_files("gcnv", "call_cnvs")),
     output:
-        **wf.get_output_files("popdel", "concat_calls"),
-    threads: wf.get_resource("popdel", "concat_calls", "threads")
+        **wf.get_output_files("gcnv", "call_cnvs"),
+    threads: wf.get_resource("gcnv", "call_cnvs", "threads")
     resources:
-        time=wf.get_resource("popdel", "concat_calls", "time"),
-        memory=wf.get_resource("popdel", "concat_calls", "memory"),
-        partition=wf.get_resource("popdel", "concat_calls", "partition"),
-        tmpdir=wf.get_resource("popdel", "concat_calls", "tmpdir"),
+        time=wf.get_resource("gcnv", "call_cnvs", "time"),
+        memory=wf.get_resource("gcnv", "call_cnvs", "memory"),
+        partition=wf.get_resource("gcnv", "call_cnvs", "partition"),
+        tmpdir=wf.get_resource("gcnv", "call_cnvs", "tmpdir"),
     log:
-        **wf.get_log_file("popdel", "concat_calls"),
+        wf.get_log_file("gcnv", "call_cnvs"),
+    params:
+        args=wf.get_params("gcnv", "call_cnvs"),
     wrapper:
-        wf.wrapper_path("popdel/concat_calls")
+        wf.wrapper_path("gcnv/call_cnvs_case_mode")
 
 
-rule sv_calling_wgs_popdel_reorder_vcf:
+rule sv_calling_wgs_gcnv_post_germline_calls:
     input:
-        unpack(wf.get_input_files("popdel", "reorder_vcf")),
+        unpack(wf.get_input_files("gcnv", "post_germline_calls")),
     output:
-        **wf.get_output_files("popdel", "reorder_vcf"),
-    threads: wf.get_resource("popdel", "reorder_vcf", "threads")
+        **wf.get_output_files("gcnv", "post_germline_calls"),
+    threads: wf.get_resource("gcnv", "post_germline_calls", "threads")
     resources:
-        time=wf.get_resource("popdel", "reorder_vcf", "time"),
-        memory=wf.get_resource("popdel", "reorder_vcf", "memory"),
-        partition=wf.get_resource("popdel", "reorder_vcf", "partition"),
-        tmpdir=wf.get_resource("popdel", "reorder_vcf", "tmpdir"),
-    wildcard_constraints:
-        index_ngs_library=r"[^\.]+",
+        time=wf.get_resource("gcnv", "post_germline_calls", "time"),
+        memory=wf.get_resource("gcnv", "post_germline_calls", "memory"),
+        partition=wf.get_resource("gcnv", "post_germline_calls", "partition"),
+        tmpdir=wf.get_resource("gcnv", "post_germline_calls", "tmpdir"),
+    log:
+        wf.get_log_file("gcnv", "post_germline_calls"),
     params:
-        ped_members=wf.substep_getattr("popdel", "get_ped_members"),
+        args=wf.get_params("gcnv", "post_germline_calls"),
+    wrapper:
+        wf.wrapper_path("gcnv/post_germline_calls_case_mode")
+
+
+rule sv_calling_wgs_gcnv_joint_germline_cnv_segmentation:
+    input:
+        unpack(wf.get_input_files("gcnv", "joint_germline_cnv_segmentation")),
+    output:
+        **wf.get_output_files("gcnv", "joint_germline_cnv_segmentation"),
+    threads: wf.get_resource("gcnv", "joint_germline_cnv_segmentation", "threads")
+    resources:
+        time=wf.get_resource("gcnv", "joint_germline_cnv_segmentation", "time"),
+        memory=wf.get_resource("gcnv", "joint_germline_cnv_segmentation", "memory"),
+        partition=wf.get_resource("gcnv", "joint_germline_cnv_segmentation", "partition"),
+        tmpdir=wf.get_resource("gcnv", "joint_germline_cnv_segmentation", "tmpdir"),
     log:
-        **wf.get_log_file("popdel", "reorder_vcf"),
+        **wf.get_log_file("gcnv", "joint_germline_cnv_segmentation"),
     wrapper:
-        wf.wrapper_path("popdel/reorder_vcf")
+        wf.wrapper_path("gcnv/joint_germline_cnv_segmentation")
diff --git a/snappy_pipeline/workflows/sv_calling_wgs/__init__.py b/snappy_pipeline/workflows/sv_calling_wgs/__init__.py
index 69d0a5cea..c08bc724f 100644
--- a/snappy_pipeline/workflows/sv_calling_wgs/__init__.py
+++ b/snappy_pipeline/workflows/sv_calling_wgs/__init__.py
@@ -4,7 +4,6 @@
 from collections import OrderedDict
 
 from biomedsheets.shortcuts import GermlineCaseSheet, is_not_background
-from snakemake.io import touch
 
 from snappy_pipeline.utils import dictify, listify
 from snappy_pipeline.workflows.abstract import (
@@ -20,6 +19,7 @@
 from snappy_pipeline.workflows.common.delly import Delly2StepPart
 from snappy_pipeline.workflows.common.gcnv.gcnv_run import RunGcnvStepPart
 from snappy_pipeline.workflows.common.manta import MantaStepPart
+from snappy_pipeline.workflows.common.melt import MeltStepPart
 from snappy_pipeline.workflows.common.sv_calling import (
     SvCallingGetLogFileMixin,
     SvCallingGetResultFilesMixin,
@@ -242,157 +242,6 @@ def get_ped_members(self, wildcards):
         )
 
 
-class MeltStepPart(
-    SvCallingGetResultFilesMixin,
-    SvCallingGetLogFileMixin,
-    ForwardSnakemakeFilesMixin,
-    ForwardResourceUsageMixin,
-    BaseStepPart,
-):
-    """MEI calling using MELT
-
-    We implement the workflow as per-pedigree calling.  Generally, this leads to consistent
-    positions within each pedigree but not necessarily across the whole cohort.
-
-    Note that MELT is not free software, so further setup is needed.
-    """
-
-    name = "melt"
-    actions = (
-        "preprocess",
-        "indiv_analysis",
-        "group_analysis",
-        "genotype",
-        "make_vcf",
-        "merge_vcf",
-        "reorder_vcf",
-    )
-
-    _resource_usage = ResourceUsage(
-        threads=6,
-        time="1-00:00:00",
-        memory=f"{int(3.75 * 1024 * 6)}M",
-    )
-    resource_usage_dict = {
-        "preprocess": _resource_usage,
-        "indiv_analysis": _resource_usage,
-        "group_analysis": _resource_usage,
-        "genotype": _resource_usage,
-        "make_vcf": _resource_usage,
-        "merge_vcf": _resource_usage,
-        "reorder_vcf": _resource_usage,
-    }
-
-    def __init__(self, parent):
-        super().__init__(parent)
-        #: All individual's primary NGS libraries
-        self.all_dna_ngs_libraries = []
-        for sheet in self.parent.shortcut_sheets:
-            for donor in sheet.donors:
-                if donor.dna_ngs_library:
-                    self.all_dna_ngs_libraries.append(donor.dna_ngs_library.name)
-        #: Linking NGS libraries to pedigree
-        self.index_ngs_library_to_pedigree = OrderedDict()
-        for sheet in filter(is_not_background, self.parent.shortcut_sheets):
-            self.index_ngs_library_to_pedigree.update(sheet.index_ngs_library_to_pedigree)
-
-    @dictify
-    def _get_input_files_preprocess(self, wildcards):
-        ngs_mapping = self.parent.sub_workflows["ngs_mapping"]
-        infix = f"{wildcards.mapper}.{wildcards.library_name}"
-        yield "bam", ngs_mapping(f"output/{infix}/out/{infix}.bam")
-
-    @dictify
-    def _get_output_files_preprocess(self):
-        # Note that mapper is not part of the output BAM file as MELT infers sample file from BAM
-        # file name instead of using sample name from BAM header.
-        prefix = "work/{mapper}.melt.preprocess.{library_name}/out/{library_name}"
-        yield "orig_bam", f"{prefix}.bam"
-        yield "orig_bai", f"{prefix}.bam.bai"
-        yield "disc_bam", f"{prefix}.bam.disc"
-        yield "disc_bai", f"{prefix}.bam.disc.bai"
-        yield "disc_fq", f"{prefix}.bam.fq"
-
-    @dictify
-    def _get_input_files_indiv_analysis(self, wildcards):
-        infix = f"{wildcards.mapper}.melt.preprocess.{wildcards.library_name}"
-        yield "orig_bam", f"work/{infix}/out/{wildcards.library_name}.bam"
-        yield "disc_bam", f"work/{infix}/out/{wildcards.library_name}.bam.disc"
-
-    @dictify
-    def _get_output_files_indiv_analysis(self):
-        infix = "{mapper}.melt.indiv_analysis.{me_type}"
-        yield "done", touch(f"work/{infix}/out/.done.{{library_name}}")
-
-    @listify
-    def _get_input_files_group_analysis(self, wildcards):
-        for library_name in self.all_dna_ngs_libraries:
-            infix = f"{wildcards.mapper}.melt.indiv_analysis.{wildcards.me_type}"
-            yield f"work/{infix}/out/.done.{library_name}"
-
-    @dictify
-    def _get_output_files_group_analysis(self):
-        yield "done", touch("work/{mapper}.melt.group_analysis.{me_type}/out/.done")
-
-    @dictify
-    def _get_input_files_genotype(self, wildcards):
-        infix_done = f"{wildcards.mapper}.melt.group_analysis.{wildcards.me_type}"
-        yield "done", f"work/{infix_done}/out/.done".format(**wildcards)
-        infix_bam = f"{wildcards.mapper}.melt.preprocess.{wildcards.library_name}"
-        yield "bam", f"work/{infix_bam}/out/{wildcards.library_name}.bam"
-
-    @dictify
-    def _get_output_files_genotype(self):
-        yield "done", touch("work/{mapper}.melt.genotype.{me_type}/out/.done.{library_name}")
-
-    @dictify
-    def _get_input_files_make_vcf(self, wildcards):
-        infix = f"{wildcards.mapper}.melt.group_analysis.{wildcards.me_type}"
-        yield "group_analysis", f"work/{infix}/out/.done"
-        paths = []
-        for library_name in self.all_dna_ngs_libraries:
-            infix = f"{wildcards.mapper}.melt.genotype.{wildcards.me_type}"
-            yield f"work/{infix}/out/.done.{library_name}"
-        yield "genotype", paths
-
-    @dictify
-    def _get_output_files_make_vcf(self):
-        infix = "{mapper}.melt.genotype.{me_type}"
-        yield "list_txt", f"work/{infix}/out/list.txt"
-        yield "done", touch(f"work/{infix}/out/.done")
-        yield "vcf", f"work/{infix}.final_comp.vcf.gz"
-        yield "vcf_tbi", f"work/{infix}.final_comp.vcf.gz.tbi"
-
-    @dictify
-    def _get_input_files_merge_vcf(self, wildcards):
-        vcfs = []
-        for me_type in self.config["melt"]["me_types"]:
-            infix = f"{wildcards.mapper}.melt.merge_vcf.{wildcards.me_type}"
-            vcfs.append(f"work/{infix}/out/{me_type}.final_comp.vcf.gz")
-        yield "vcf", vcfs
-
-    @dictify
-    def _get_output_files_merge_vcf(self):
-        infix = "{mapper}.melt.merge_vcf"
-        yield "vcf", f"work/{infix}/out/{infix}.vcf.gz"
-        yield "vcf_md5", f"work/{infix}/out/{infix}.vcf.gz.md5"
-        yield "vcf_tbi", f"work/{infix}/out/{infix}.vcf.gz.tbi"
-        yield "vcf_tbi_md5", f"work/{infix}/out/{infix}.vcf.gz.tbi.md5"
-
-    @dictify
-    def _get_input_files_reorder_vcf(self, wildcards):
-        infix = f"{wildcards.mapper}.melt.merge_vcf"
-        yield "vcf", f"work/{infix}/out/{infix}.vcf.gz"
-
-    @dictify
-    def _get_output_files_reorder_vcf(self):
-        infix = "{mapper}.melt.{index_library_name}"
-        yield "vcf", f"work/{infix}/out/{infix}.vcf.gz"
-        yield "vcf_md5", f"work/{infix}/out/{infix}.vcf.gz.md5"
-        yield "vcf_tbi", f"work/{infix}/out/{infix}.vcf.gz.tbi"
-        yield "vcf_tbi_md5", f"work/{infix}/out/{infix}.vcf.gz.tbi.md5"
-
-
 class Sniffles2StepPart(BaseStepPart):
     """WGS SV identification using Sniffles 2"""
 
@@ -468,10 +317,10 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir)
             (
                 Delly2StepPart,
                 MantaStepPart,
-                PopDelStepPart,
+                #               PopDelStepPart,
                 GcnvWgsStepPart,
                 MeltStepPart,
-                Sniffles2StepPart,
+                #               Sniffles2StepPart,
                 WritePedigreeStepPart,
             )
         )
diff --git a/snappy_wrappers/wrappers/melt/genotype/wrapper.py b/snappy_wrappers/wrappers/melt/genotype/wrapper.py
index ba386778c..1b2a70434 100644
--- a/snappy_wrappers/wrappers/melt/genotype/wrapper.py
+++ b/snappy_wrappers/wrappers/melt/genotype/wrapper.py
@@ -12,7 +12,7 @@
 set -x
 # -----------------------------------------------------------------------------
 
-JAR={snakemake.config[step_config][sv_calling_targeted][melt][jar_file]}
+JAR={melt_config[jar_file]}
 ME_REFS={melt_config[me_refs_path]}
 ME_INFIX={melt_config[me_refs_infix]}
 
diff --git a/snappy_wrappers/wrappers/melt/group_analysis/wrapper.py b/snappy_wrappers/wrappers/melt/group_analysis/wrapper.py
index a99e4959b..98f5384d3 100644
--- a/snappy_wrappers/wrappers/melt/group_analysis/wrapper.py
+++ b/snappy_wrappers/wrappers/melt/group_analysis/wrapper.py
@@ -12,7 +12,7 @@
 set -x
 # -----------------------------------------------------------------------------
 
-JAR={snakemake.config[step_config][sv_calling_targeted][melt][jar_file]}
+JAR={melt_config[jar_file]}
 ME_REFS={melt_config[me_refs_path]}
 ME_INFIX={melt_config[me_refs_infix]}
 
diff --git a/snappy_wrappers/wrappers/melt/indiv_analysis/wrapper.py b/snappy_wrappers/wrappers/melt/indiv_analysis/wrapper.py
index 6ebed325c..34d41106e 100644
--- a/snappy_wrappers/wrappers/melt/indiv_analysis/wrapper.py
+++ b/snappy_wrappers/wrappers/melt/indiv_analysis/wrapper.py
@@ -13,7 +13,7 @@
 set -x
 # -----------------------------------------------------------------------------
 
-JAR={snakemake.config[step_config][sv_calling_targeted][melt][jar_file]}
+JAR={melt_config[jar_file]}
 ME_REFS={melt_config[me_refs_path]}
 ME_INFIX={melt_config[me_refs_infix]}
 
diff --git a/snappy_wrappers/wrappers/melt/make_vcf/wrapper.py b/snappy_wrappers/wrappers/melt/make_vcf/wrapper.py
index b78b173de..1c0437827 100644
--- a/snappy_wrappers/wrappers/melt/make_vcf/wrapper.py
+++ b/snappy_wrappers/wrappers/melt/make_vcf/wrapper.py
@@ -12,7 +12,7 @@
 set -x
 # -----------------------------------------------------------------------------
 
-JAR={snakemake.config[step_config][sv_calling_targeted][melt][jar_file]}
+JAR={melt_config[jar_file]}
 ME_REFS={melt_config[me_refs_path]}
 ME_INFIX={melt_config[me_refs_infix]}
 
diff --git a/snappy_wrappers/wrappers/melt/preprocess/wrapper.py b/snappy_wrappers/wrappers/melt/preprocess/wrapper.py
index 37a37d76e..076a52615 100644
--- a/snappy_wrappers/wrappers/melt/preprocess/wrapper.py
+++ b/snappy_wrappers/wrappers/melt/preprocess/wrapper.py
@@ -2,6 +2,8 @@
 
 __author__ = "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>"
 
+melt_config = snakemake.config["step_config"][snakemake.params.step_key]["melt"]
+
 shell(
     r"""
 # -----------------------------------------------------------------------------
@@ -13,7 +15,7 @@
 ln -sr {snakemake.input.bam} {snakemake.output.orig_bam}
 ln -sr {snakemake.input.bai} {snakemake.output.orig_bai}
 
-JAR={snakemake.config[step_config][sv_calling_targeted][melt][jar_file]}
+JAR={melt_config[jar_file]}
 
 java -Xmx4G -jar $JAR \
     Preprocess \