├── .devcontainer └── devcontainer.json ├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── branch.yml │ ├── build-docs.yml │ ├── ci.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix-linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ └── release-announcements.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── bedgovcf │ ├── qdnaseq.yaml │ └── wisecondorx.yaml ├── email_template.html ├── email_template.txt ├── manta_config.ini ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-centerformedicalgeneticsghent-nf-cmgg-structural_logo_light.png ├── samplesheet.csv ├── samplesheet_big.csv ├── samplesheet_full.csv ├── schema_input.json ├── sendmail_template.txt ├── slackreport.json ├── svync │ ├── delly.yaml │ ├── gridss.yaml │ ├── manta.yaml │ └── smoove.yaml ├── test.npz ├── test.ped ├── test_local.ped ├── test_wisecondorx_reference.npz ├── vcfanno │ ├── 1KGP_3202.toml │ ├── CREs_v1.toml │ ├── IRD_v9.toml │ ├── RetNetCNV_v1.toml │ ├── RetNet_v6.toml │ ├── all_v8.toml │ ├── annotsv.toml │ ├── dbVar.toml │ ├── nstd166.toml │ ├── retina_scale.toml │ └── rpe_scale.toml └── vcfanno_unused │ └── goNL_AF_genotyped_SVs.toml ├── bin ├── fix_callers.py └── viola_standardize.py ├── conf ├── base.config ├── igenomes.config ├── modules.config ├── test.config ├── test_big.config └── test_full.config ├── docs ├── CITATIONS.md ├── images │ ├── metro_map.png │ ├── metro_map.svg │ ├── pipeline_logo.png │ ├── pipeline_logo.svg │ ├── pipeline_logo_full.png │ └── pipeline_logo_full.svg ├── index.md ├── output.md ├── parameters.md └── usage.md ├── lib ├── CustomChannelOperators.groovy ├── DynamicContainers.groovy └── GlobalVariables.groovy ├── main.nf ├── mkdocs.yml ├── modules.json ├── modules ├── local │ ├── bcftools │ │ ├── consensus_reheader │ │ │ ├── environment.yml │ │ │ └── main.nf │ │ └── split_by_svtype │ │ │ ├── environment.yml │ │ │ └── main.nf │ ├── fix_callers │ │ ├── Dockerfile │ │ ├── environment.yaml │ │ └── main.nf │ └── qdnaseq │ │ ├── main.nf │ │ └── templates │ │ └── qDNAseq.R └── nf-core │ ├── annotsv │ ├── annotsv │ │ ├── annotsv-annotsv.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── installannotations │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── bcftools │ ├── annotate │ │ ├── bcftools-annotate.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── bcf.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── tags.yml │ │ │ └── vcf.config │ ├── concat │ │ ├── bcftools-concat.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── filter │ │ ├── bcftools-filter.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── bedgovcf │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── bwa │ └── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── delly │ └── call │ │ ├── delly-call.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── tags.yml │ │ └── vcf.config │ ├── ensemblvep │ ├── download │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ └── vep │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── tab.gz.config │ │ ├── tags.yml │ │ └── vcf.config │ ├── expansionhunter │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── gawk │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── nextflow_with_program_file.config │ │ └── tags.yml │ ├── gridss │ └── gridss │ │ ├── environment.yml │ │ ├── gridss-gridss.diff │ │ ├── main.nf │ │ └── meta.yml │ ├── jasminesv │ ├── environment.yml │ ├── jasminesv.diff │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── iris.config │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── normalize.config │ │ └── tags.yml │ ├── manta │ ├── convertinversion │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── germline │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── ngsbits │ └── samplegender │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── samtools │ ├── convert │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── samtools-convert.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── faidx │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow2.config │ │ │ └── tags.yml │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── index.config │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── smoove │ └── call │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── svync │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── tabix │ ├── bgziptabix │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── tabix_csi.config │ │ │ ├── tabix_tbi.config │ │ │ └── tags.yml │ └── tabix │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── tabix_bed.config │ │ ├── tabix_gff.config │ │ ├── tabix_vcf_csi.config │ │ ├── tabix_vcf_tbi.config │ │ └── tags.yml │ ├── untar │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── vcfanno │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ └── wisecondorx │ ├── convert │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ └── predict │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── tags.yml ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── pyproject.toml ├── subworkflows ├── local │ ├── bam_cnv_calling │ │ └── main.nf │ ├── bam_prepare_samtools │ │ └── main.nf │ ├── bam_repeat_estimation_expansionhunter │ │ └── main.nf │ ├── bam_sv_calling │ │ └── main.nf │ ├── bam_variant_calling_delly │ │ └── main.nf │ ├── bam_variant_calling_gridss │ │ └── main.nf │ ├── bam_variant_calling_manta │ │ └── main.nf │ ├── bam_variant_calling_qdnaseq │ │ └── main.nf │ ├── bam_variant_calling_smoove │ │ └── main.nf │ ├── bam_variant_calling_wisecondorx │ │ └── main.nf │ ├── utils_nfcore_structural_pipeline │ │ └── main.nf │ ├── vcf_annotate_vep_annotsv_vcfanno │ │ └── main.nf │ ├── vcf_concat_bcftools │ │ └── main.nf │ ├── vcf_merge_callers_jasmine │ │ └── main.nf │ └── vcf_merge_family_jasmine │ │ └── main.nf └── nf-core │ ├── utils_nextflow_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ ├── nextflow.config │ │ └── tags.yml │ ├── utils_nfcore_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ ├── main.workflow.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml │ └── utils_nfvalidation_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow_schema.json │ └── tags.yml ├── tests ├── inputs │ └── samplesheet_family.csv ├── nextflow.config ├── pipeline │ ├── all_types │ │ ├── all.nf.test │ │ └── all.nf.test.snap │ ├── cnv │ │ ├── cnv.nf.test │ │ └── cnv.nf.test.snap │ ├── duplicates │ │ ├── duplicates.nf.test │ │ ├── duplicates.nf.test.snap │ │ └── samplesheet_duplicate2.csv │ ├── families │ │ ├── families.nf.test │ │ ├── families.nf.test.snap │ │ ├── samplesheet_family2_sample1.csv │ │ └── samplesheet_family3.csv │ ├── repeats │ │ ├── repeats.nf.test │ │ └── repeats.nf.test.snap │ └── sv │ │ ├── sv.nf.test │ │ └── sv.nf.test.snap ├── samplesheet.csv └── subworkflows │ └── local │ ├── bam_cnv_calling │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config │ ├── bam_prepare_samtools │ ├── main.nf.test │ └── main.nf.test.snap │ ├── bam_repeat_estimation_expansionhunter │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config │ ├── bam_sv_calling │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config │ ├── bam_variant_calling_delly │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config │ ├── bam_variant_calling_gridss │ ├── main.nf.test.disabled │ └── nextflow.config │ ├── bam_variant_calling_manta │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config │ ├── bam_variant_calling_qdnaseq │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config │ ├── bam_variant_calling_smoove │ ├── main.nf.test │ └── main.nf.test.snap │ ├── bam_variant_calling_wisecondorx │ ├── main.nf.test │ └── main.nf.test.snap │ ├── vcf_annotate_vep_annotsv_vcfanno │ ├── main.nf.test │ ├── main.nf.test.snap │ 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