├── .devcontainer ├── devcontainer.json └── setup.sh ├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CODEOWNERS ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ ├── feature_request.yml │ └── user_story.yml ├── PULL_REQUEST_TEMPLATE.md ├── actions │ ├── find-tests │ │ └── action.yml │ ├── get-shards │ │ └── action.yml │ └── nf-test │ │ └── action.yml └── workflows │ ├── awstest.yml │ ├── branch.yml │ ├── build-docs.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix-linting.yml │ ├── fix_linting.yml │ ├── keep_a_changelog.yml │ ├── linting │ ├── linting.yml │ ├── linting_comment.yml │ ├── nf-test.yml │ ├── template-version-comment.yml │ └── template_version_comment.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── .vscode └── settings.json ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── cadd_to_vcf_header_-1.0-.txt ├── echtvar_snv_databases.csv ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc_config.yml ├── samplesheet.csv ├── samplesheet_multisample_bam.csv ├── samplesheet_multisample_ont_bam.csv ├── samplesheet_ont.csv ├── samplesheet_same_sample_and_family_id.csv ├── schema_hgnc_ids.json ├── schema_input.json ├── schema_snp_db.json ├── schema_vep_plugin_files.json ├── sendmail_template.txt ├── slackreport.json ├── software_references.yml ├── svdb_query_vcf_schema.json └── vep_plugin_files_schema.json ├── bin ├── add_most_severe_consequence.py ├── add_most_severe_pli.py ├── clean_sniffles.py ├── merge_json_sample_files_into_family.py └── split_bed_chunks.py ├── conf ├── base.config └── modules │ ├── align_assemblies.config │ ├── annotate_cadd.config │ ├── annotate_consequence_pli.config │ ├── annotate_snvs.config │ ├── annotate_svs.config │ ├── bam_infer_sex.config │ ├── call_paralogs.config │ ├── call_repeat_expansions_strdust.config │ ├── call_repeat_expansions_trgt.config │ ├── call_snvs.config │ ├── call_svs.config │ ├── chromograph.config │ ├── convert_input_files.config │ ├── filter_variants.config │ ├── genome_assembly.config │ ├── gvcf_glnexus_norm_variants.config │ ├── methylation.config │ ├── nallo.config │ ├── phasing.config │ ├── prepare_references.config │ ├── qc_aligned_reads.config │ ├── qc_snvs.config │ ├── rank_variants.config │ ├── scatter_genome.config │ ├── vcf_concat_norm_variants.config │ └── vcf_concat_sort_variants.config ├── docs ├── CITATIONS.md ├── README.md ├── images │ ├── nallo_dark.png │ ├── nallo_light.png │ ├── nallo_metromap.png │ └── nallo_metromap.svgz ├── index.md ├── output.md ├── parameters.md └── usage.md ├── main.nf ├── mkdocs.yml ├── modules.json ├── modules ├── local │ ├── add_found_in_tag │ │ ├── environment.yml │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── add_most_severe_consequence │ │ └── main.nf │ ├── add_most_severe_pli │ │ └── main.nf │ ├── build_intervals │ │ └── main.nf │ ├── clean_sniffles │ │ └── main.nf │ ├── create_pedigree_file │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── create_samples_file │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── create_samples_haplotypes_file │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── echtvar │ │ └── anno │ │ │ ├── Dockerfile │ │ │ ├── README.md │ │ │ └── main.nf │ ├── hiphase │ │ └── main.nf │ ├── merge_json │ │ └── main.nf │ ├── pacbio │ │ └── hificnv │ │ │ └── main.nf │ └── whatshap │ │ ├── haplotag │ │ └── main.nf │ │ ├── phase │ │ └── main.nf │ │ └── stats │ │ └── main.nf └── nf-core │ ├── bcftools │ ├── annotate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── bcf.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── vcf.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── concat │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── bcf.config │ │ │ ├── bcf_gz.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── nextflow.gvcf.config │ │ │ ├── vcf.config │ │ │ ├── vcf_gz.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── norm │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.bcf.config │ │ │ ├── nextflow.bcf_gz.config │ │ │ ├── nextflow.config │ │ │ ├── nextflow.vcf.config │ │ │ ├── nextflow.vcf_gz.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── pluginsplit │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── query │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── reheader │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── bcf.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── vcf.config │ │ │ ├── vcf.gz.config │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── roh │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── vcf_gz_index.config │ │ │ ├── vcf_gz_index_csi.config │ │ │ └── vcf_gz_index_tbi.config │ ├── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── view │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── vcf_gz_index.config │ │ ├── vcf_gz_index_csi.config │ │ └── vcf_gz_index_tbi.config │ ├── bedtools │ ├── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── split │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── cadd │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── cat │ └── fastq │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── chromograph │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── cramino │ ├── cramino.diff │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── deepvariant │ ├── rundeepvariant │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── vcfstatsreport │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── ensemblvep │ ├── filtervep │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ ├── tab.gz.config │ │ │ └── vcf.config │ └── vep │ │ ├── ensemblvep-vep.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── tab.gz.config │ │ └── vcf.config │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── gawk │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── genmod │ ├── annotate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── compound │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── models │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── score │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── gfastats │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── glnexus │ ├── environment.yml │ ├── glnexus.diff │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── hifiasm │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── longphase │ ├── haplotag │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── phase │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── minimap2 │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── modkit │ ├── bedmethyltobigwig │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── modkit-bedmethyltobigwig.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── pileup │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.traditional.config │ │ ├── nextflow.traditional_hp.config │ │ ├── nextflow.traditional_hp_bedgraph.config │ │ └── tags.yml │ ├── mosdepth │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── quantized.config │ │ ├── threshold.config │ │ └── window.config │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── paraphase │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── nextflow.csi_index.config │ ├── peddy │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── rhocall │ └── viz │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── rhocall-viz.diff │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── samtools │ ├── convert │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── samtools-convert.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── faidx │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── nextflow2.config │ ├── fastq │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── import │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── samtools-merge.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── nextflow_cram.config │ └── view │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── bam.config │ │ ├── bam_index.config │ │ ├── cram_index.config │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── sawfish │ ├── discover │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── sawfish_discover.config │ └── jointcall │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── sawfish_jointcall.config │ ├── severus │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── sniffles │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── sniffles.diff │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── somalier │ ├── extract │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── somalier-extract.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── relate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── somalier-relate.diff │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── splitubam │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── stranger │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── strdust │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── svdb │ ├── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── query │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── tabix │ ├── bgzip │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── bgzip_compress.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── vcf_none.config │ ├── bgziptabix │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── tabix_csi.config │ │ │ └── tabix_tbi.config │ └── 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 │ ├── tagbam │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── tiddit │ └── cov │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── trgt │ ├── genotype │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── untar │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ └── untar.diff │ └── yak │ └── count │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── tests │ ├── main.nf.test │ └── main.nf.test.snap │ └── yak-count.diff ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── pyproject.toml ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── align_assemblies │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── annotate_cadd │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── annotate_consequence_pli │ │ └── main.nf │ ├── annotate_snvs │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── annotate_svs │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── bam_infer_sex │ │ └── main.nf │ ├── call_paralogs │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── call_repeat_expansions_strdust │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── call_repeat_expansions_trgt │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── call_snvs │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── call_svs │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── chromograph │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── convert_input_files │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── genome_assembly │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── gvcf_glnexus_norm_variants │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── methylation │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── phasing │ │ └── main.nf │ ├── prepare_references │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── qc_aligned_reads │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── qc_snvs │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── rank_variants │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── scatter_genome │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── utils_nfcore_nallo_pipeline │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.function.nf.test │ │ │ └── main.function.nf.test.snap │ ├── vcf_concat_norm_variants │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── vcf_concat_sort_variants │ │ ├── main.nf │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config └── 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 │ ├── 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 │ ├── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── nextflow.config │ │ └── nextflow_schema.json │ └── vcf_filter_bcftools_ensemblvep │ ├── main.nf │ ├── meta.yml │ ├── nextflow.config │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config ├── tests ├── .nftignore ├── .nftignore_unstable_alignments ├── .nftignore_unstable_variants ├── nextflow.config ├── samplesheet.nf.test ├── samplesheet.nf.test.snap ├── samplesheet_multisample_bam.nf.test ├── samplesheet_multisample_bam.nf.test.snap ├── samplesheet_multisample_ont_bam.nf.test ├── samplesheet_multisample_ont_bam.nf.test.snap ├── samplesheet_stub.nf.test ├── samplesheet_stub.nf.test.snap ├── samplesheet_target_regions_null.nf.test └── samplesheet_target_regions_null.nf.test.snap ├── tower.yml └── workflows └── nallo.nf /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- 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