Conflict after changes to Delly2 DAG in WGS SV Annotation

[eudesbarbosa]

Issue
After changes to Delly DAG in WGS SV Calling, it no longer outputs an merged file, *.delly2.merge_genotypes*.
Error:

11-29 21:51 snakemake.logging WARNING  Building DAG of jobs...
MissingInputException in rule wgs_sv_annotation_vcf_sv_filter  in line 71 of /path/to/snappy-pipeline/snappy_pipeline/workflows/wgs_sv_annotation/Snakefile:
Missing input files for rule wgs_sv_annotation_vcf_sv_filter:
    output: work/bwa.delly2.annotated.<LIBRARY_NAME>/out/bwa.delly2.annotated.<LIBRARY_NAME>.vcf.gz, work/bwa.delly2.annotated.<LIBRARY_NAME>/out/bwa.delly2.annotated.<LIBRARY_NAME>.vcf.gz.tbi, work/bwa.delly2.annotated.<LIBRARY_NAME>/out/bwa.delly2.annotated.<LIBRARY_NAME>.vcf.gz.md5, work/bwa.delly2.annotated.<LIBRARY_NAME>/out/bwa.delly2.annotated.<LIBRARY_NAME>.vcf.gz.tbi.md5
    wildcards: mapper=bwa, caller=delly2, index_ngs_library=<LIBRARY_NAME>
    affected files:
        /path/to/wgs_sv_calling/work/bwa.delly2.merge_genotypes/out/bwa.delly2.merge_genotypes.bcf.csi
        /path/to/wgs_sv_calling/work/bwa.delly2.merge_genotypes/out/bwa.delly2.merge_genotypes.bcf
11-29 21:51 snakemake.logging ERROR    MissingInputException in rule wgs_sv_annotation_vcf_sv_filter  in line 71 of /path/to/snappy-pipeline/snappy_pipeline/workflows/wgs_sv_annotation/Snakefile:
Missing input files for rule wgs_sv_annotation_vcf_sv_filter:
    output: work/bwa.delly2.annotated.<LIBRARY_NAME>/out/bwa.delly2.annotated.<LIBRARY_NAME>.vcf.gz, work/bwa.delly2.annotated.<LIBRARY_NAME>/out/bwa.delly2.annotated.<LIBRARY_NAME>.vcf.gz.tbi, work/bwa.delly2.annotated.<LIBRARY_NAME>/out/bwa.delly2.annotated.<LIBRARY_NAME>.vcf.gz.md5, work/bwa.delly2.annotated.<LIBRARY_NAME>/out/bwa.delly2.annotated.<LIBRARY_NAME>.vcf.gz.tbi.md5
    wildcards: mapper=bwa, caller=delly2, index_ngs_library=<LIBRARY_NAME>
    affected files:
        /path/to/wgs_sv_calling/work/bwa.delly2.merge_genotypes/out/bwa.delly2.merge_genotypes.bcf.csi
        /path/to/wgs_sv_calling/work/bwa.delly2.merge_genotypes/out/bwa.delly2.merge_genotypes.bcf

To Reproduce
Required relevant config parts to reproduce the behavior:

  wgs_sv_annotation:
    tool_ngs_mapping_variant_calling: bwa 
    tool_variant_calling: gatk_hc
    tools_ngs_mapping: [bwa]
    tools_wgs_sv_calling: [delly2]

  wgs_sv_calling:
    path_ngs_mapping: ../ngs_mapping
    tools:
      dna:
      - delly2
      - manta

  wgs_sv_export:
    release: GRCh37  # REQUIRED: default 'GRCh37'
    path_refseq_ser: ...

Called with cubi-tk snappy kickoff

Expected behavior
The correct file name convention should be set in wgs_sv_annotation.
From snappy-pipeline/snappy_pipeline/workflows/wgs_sv_annotation/__init__.py:

class VcfSvFilterStepPart(BaseStepPart):

     ...

    def get_input_files(self, action):
        """Return path to pedigree input file"""
        assert action == "run"

        @dictify
        def input_function(wildcards):
            if wildcards.caller == "popdel":
                name_pattern = "internal.concat_calls"
                key_ext = {"bcf": ".vcf.gz", "csi": ".vcf.gz.tbi"}
            else:  # delly2
                name_pattern = "merge_genotypes"
                key_ext = {"bcf": ".bcf", "csi": ".bcf.csi"}

            tpl = "work/write_pedigree.{index_ngs_library}/out/{index_ngs_library}.ped"
            yield "ped", tpl.format(**wildcards)
            # TODO: make work for non-Delly?
            tpl = (
                "work/{mapper}.{caller}.{index_ngs_library}/out/"
                "{mapper}.{caller}.{index_ngs_library}"
            )
            # SVs
            wgs_sv_calling = self.parent.sub_workflows["wgs_sv_calling"]
            for key, ext in key_ext.items():
                yield "sv_" + key, wgs_sv_calling(
                    tpl.replace("{index_ngs_library}", name_pattern) + ext
                ).format(**wildcards)

Additional context
Changed output and removed Delly dependency from WGS SV Annotation: #188
WGS SV Export and Annotation have a dependency in kickoff based on PopDel usage, not Delly. But I assume still need to be called...?

[eudesbarbosa]

CC @Nicolai-vKuegelgen