├── .devcontainer ├── devcontainer.json └── setup.sh ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md ├── actions │ ├── get-shards │ │ └── action.yml │ └── nf-test │ │ └── action.yml └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix_linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── nf-test.yml │ ├── release-announcements.yml │ └── template-version-comment.yml ├── .gitignore ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── .vscode └── settings.json ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc_config.yml ├── nf-core-rnavar_logo_light.png ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin └── remove_unknown_regions.py ├── conf ├── base.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── modules │ ├── annotate.config │ └── prepare_cache.config ├── test.config └── test_full.config ├── docs ├── README.md ├── images │ ├── alignment_star_mapping_stats.png │ ├── fastqc_gc_content.png │ ├── fastqc_length_dist.png │ ├── fastqc_mean_qual_score_dist.png │ ├── fastqc_overall_status.png │ ├── fastqc_seq_counts.png │ ├── multiqc_report.png │ ├── nf-core-rnavar_logo_dark.png │ ├── nf-core-rnavar_logo_light.png │ ├── read_markduplicates_stats.png │ ├── snpeff_variant_quality.png │ ├── snpeff_variants_by_effect_types.png │ ├── snpeff_variants_by_impact.png │ ├── snpeff_variants_by_region.png │ ├── vep_general_stats.png │ ├── vep_pph_summary.png │ └── vep_sift_summary.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── gtf2bed │ │ ├── environment.yml │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── remove_unknown_regions │ │ ├── environment.yml │ │ ├── main.nf │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap └── nf-core │ ├── bcftools │ └── annotate │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── bedtools │ ├── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── cat │ └── fastq │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── ensemblvep │ ├── download │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── vep │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── gatk4 │ ├── applybqsr │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── baserecalibrator │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── bedtointervallist │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── combinegvcfs │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── createsequencedictionary │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── haplotypecaller │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── indexfeaturefile │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── intervallisttools │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── mergevcfs │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── splitncigarreads │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── variantfiltration │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── gffread │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── mosdepth │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── picard │ └── markduplicates │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── samtools │ ├── convert │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── faidx │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── flagstat │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── idxstats │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── merge │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── seq2hla │ ├── environment.yml │ ├── main.nf │ └── meta.yml │ ├── snpeff │ ├── download │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── snpeff │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── star │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── genomegenerate │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── indexversion │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── tabix │ ├── bgziptabix │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── tabix │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ ├── umitools │ └── extract │ │ ├── environment.yml │ │ ├── main.nf │ │ └── meta.yml │ └── untar │ ├── environment.yml │ ├── main.nf │ └── meta.yml ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── annotation_cache_initialisation │ │ └── main.nf │ ├── cram_qc_mosdepth_samtools │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── download_cache_snpeff_vep │ │ └── main.nf │ ├── prepare_alignment │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── prepare_genome │ │ ├── main.nf │ │ └── tests │ │ │ ├── functions.nf.test │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── recalibrate │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── splitncigar │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── utils_nfcore_rnavar_pipeline │ │ └── main.nf │ └── vcf_annotate_all │ │ └── main.nf └── nf-core │ ├── bam_markduplicates_picard │ ├── main.nf │ └── meta.yml │ ├── bam_sort_stats_samtools │ ├── main.nf │ └── meta.yml │ ├── bam_stats_samtools │ ├── main.nf │ └── meta.yml │ ├── fastq_align_star │ ├── main.nf │ ├── meta.yml │ └── nextflow.config │ ├── vcf_annotate_ensemblvep │ ├── main.nf │ └── meta.yml │ └── vcf_annotate_snpeff │ ├── main.nf │ └── meta.yml ├── tests ├── .nftignore ├── all_inputs.nf.test ├── all_inputs.nf.test.snap ├── annotation_bcfann.nf.test ├── annotation_bcfann.nf.test.snap ├── annotation_merge.nf.test ├── annotation_merge.nf.test.snap ├── annotation_snpeff.nf.test ├── annotation_vep.nf.test ├── bam_csi.nf.test ├── bam_csi.nf.test.snap ├── bam_input.nf.test ├── bam_input.nf.test.snap ├── config │ ├── bcfann_test_columns.txt │ └── 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