├── .devcontainer └── devcontainer.json ├── .gitattributes ├── .github ├── .dockstore.yml ├── CODEOWNERS ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md ├── actions │ ├── get-shards │ │ └── action.yml │ └── nf-test │ │ └── action.yml └── workflows │ ├── branch.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix_linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── nf-test.yml │ └── template-version-comment.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── 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 ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt ├── slackreport.json ├── tomte_logo_light.png └── vep_plugin_files_schema.json ├── bin ├── BootstrapAnn.py ├── calculate_perc_mapping.py ├── drop_config.py ├── drop_filter_results.py ├── drop_sample_annot.py ├── drop_sample_annot_exported_counts.py ├── get_rrna_transcripts.py ├── gtf2bed └── sj2bed.py ├── conf ├── base.config ├── igenomes.config ├── igenomes_ignored.config ├── modules │ ├── alignment.config │ ├── allele_specific_calling.config │ ├── analyse_transcripts.config │ ├── annotate_snv.config │ ├── bam_qc.config │ ├── call_variants.config │ ├── download_references.config │ ├── general_tomte.config │ ├── igv_tracks.config │ └── prepare_references.config ├── test.config └── test_full.config ├── docs ├── README.md ├── images │ ├── tomte_logo_dark.png │ ├── tomte_logo_light.png │ ├── tomte_pipeline_metromap.png │ └── tomte_pipeline_metromap.svg ├── output.md ├── parameters.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── add_found_in_tag │ │ ├── environment.yml │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── bootstrapann │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── build_vep_cache │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── create_pedigree_file │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── download │ │ ├── gencode_download │ │ │ ├── main.nf │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ └── main.nf.test.snap │ │ ├── vep_gnomad_download │ │ │ ├── main.nf │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ └── main.nf.test.snap │ │ └── wget_download │ │ │ ├── main.nf │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── drop │ │ ├── drop_config_runAE │ │ │ ├── main.nf │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── nextflow.config │ │ ├── drop_config_runAS │ │ │ ├── main.nf │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── nextflow.config │ │ ├── drop_config_runMAE │ │ │ ├── main.nf │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── nextflow.config │ │ ├── drop_filter_results │ │ │ ├── main.nf │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── nextflow.config │ │ ├── drop_put_together_exported_counts │ │ │ ├── main.nf │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── nextflow.config │ │ └── drop_sample_annot │ │ │ ├── main.nf │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── estimate_hb_perc │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── get_rrna_transcripts │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── junction_track │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── rename_files │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── rna_downsample │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── rna_subsample_region │ │ ├── main.nf │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap └── nf-core │ ├── bcftools │ ├── 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 │ ├── mpileup │ │ ├── bcftools-mpileup.diff │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.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 │ ├── 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 │ ├── cat │ └── fastq │ │ ├── environment.yml │ │ ├── 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 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ ├── tab.gz.config │ │ └── vcf.config │ ├── fastp │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.interleaved.config │ │ └── nextflow.save_failed.config │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── gatk4 │ ├── asereadcounter │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── bedtointervallist │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── createsequencedictionary │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── haplotypecaller │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── splitncigarreads │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── variantfiltration │ │ ├── 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 │ ├── gffcompare │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── gffread │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow-fasta.config │ │ ├── nextflow-gff3.config │ │ └── nextflow.config │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── peddy │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── peddy.diff │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── picard │ ├── collectinsertsizemetrics │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── picard-collectinsertsizemetrics.diff │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── collectrnaseqmetrics │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── picard-collectrnaseqmetrics.diff │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── salmon │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── quant │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── salmon-quant.diff │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── samtools │ ├── convert │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── 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 │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── view │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── bam.config │ │ ├── bam_index.config │ │ ├── cram_index.config │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── star │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.arriba.config │ │ │ ├── nextflow.config │ │ │ └── nextflow.starfusion.config │ └── genomegenerate │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── stringtie │ └── stringtie │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── tabix │ ├── 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 │ ├── ucsc │ ├── gtftogenepred │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── wigtobigwig │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ └── untar │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ └── main.nf.test.snap ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── pyproject.toml ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── alignment │ │ ├── main.nf │ │ └── tests │ │ │ ├── alignment.nf.test │ │ │ ├── alignment.nf.test.snap │ │ │ └── nextflow.config │ ├── allele_specific_calling │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── analyse_transcripts │ │ ├── main.nf │ │ └── tests │ │ │ ├── analyse_transcripts.nf.test │ │ │ ├── analyse_transcripts.nf.test.snap │ │ │ └── nextflow.config │ ├── annotate_snv │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── bam_qc │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── call_variants │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── call_variants_gatk │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── download_references │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── igv_tracks │ │ ├── main.nf │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ ├── prepare_references │ │ ├── main.nf │ │ └── tests │ │ │ ├── nextflow.config │ │ │ ├── prepare_references.nf.test │ │ │ └── prepare_references.nf.test.snap │ └── utils_nfcore_tomte_pipeline │ │ └── 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 │ └── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow.config │ └── nextflow_schema.json ├── test_data ├── ACC5963A1.bam ├── ACC5963A1.bam.bai ├── ACC5963A1_split_rmdup_info.vcf.gz ├── ACC5963A1_split_rmdup_info.vcf.gz.tbi ├── ACC5963A1_sub_1.fastq.gz ├── ACC5963A1_sub_2.fastq.gz ├── ACC5963A2_sub_1.fastq.gz ├── ACC5963A2_sub_2.fastq.gz ├── ACC5963A3.cram ├── ACC5963A3.cram.crai ├── ACC5963A3_split_rmdup_info.vcf.gz ├── ACC5963A3_split_rmdup_info.vcf.gz.tbi ├── drop_data │ ├── geneCounts.tsv.gz │ ├── k_j_counts.tsv.gz │ ├── k_theta_counts.tsv.gz │ ├── mock_gene_panel.tsv │ ├── n_psi3_counts.tsv.gz │ ├── n_psi5_counts.tsv.gz │ ├── n_theta_counts.tsv.gz │ └── sampleAnnotation.tsv ├── grch37_chr21.fa.gz ├── grch37_chr21.gtf.gz ├── grch37_chr21_transcripts.fa.gz ├── qc_vcf_1000G_hg19_chr21.vcf.gz ├── qc_vcf_1000G_hg19_chr21.vcf.gz.tbi ├── samplesheet_chr21.csv ├── samplesheet_chr21_no_vcf.csv ├── subsample.bed ├── test_ACC5963A1.vcf.gz ├── test_ACC5963A1.vcf.gz.tbi ├── vep_to_download.csv └── vep_to_download_37.csv ├── tests ├── .nftignore ├── .nftignore_unstable_name ├── default.nf.test ├── default.nf.test.snap ├── nextflow.config ├── skip_main.nf.test └── skip_main.nf.test.snap ├── tower.yml └── workflows └── tomte.nf /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/genomic-medicine-sweden/tomte/HEAD/.devcontainer/devcontainer.json -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 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