├── .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 │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── fix-linting.yml │ ├── linting.yml │ └── linting_comment.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .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 ├── nf-core-nanoseq_logo_light.png ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── JAFFAL.groovy ├── check_samplesheet.py ├── create_yml.py ├── gtf2bed ├── run_bambu.r ├── run_deseq2.r └── run_dexseq.r ├── conf ├── base.config ├── igenomes.config ├── modules.config ├── test.config ├── test_full.config ├── test_nodx_noaln.config ├── test_nodx_rnamod.config ├── test_nodx_stringtie.config └── test_nodx_vc.config ├── docs ├── README.md ├── images │ ├── mqc_fastqc_adapter.png │ ├── mqc_fastqc_counts.png │ ├── mqc_fastqc_quality.png │ ├── mqc_samtools_stats_plot.png │ ├── nanoplot_readlengthquality.png │ ├── nanoseq_subwaymap_v3.1.png │ ├── nanoseq_subwaymap_v3.1.svg │ ├── nf-core-nanoseq_logo_dark.png │ └── nf-core-nanoseq_logo_light.png ├── output.md └── usage.md ├── lib ├── NfcoreSchema.groovy ├── NfcoreTemplate.groovy ├── Utils.groovy ├── WorkflowMain.groovy ├── WorkflowNanoseq.groovy └── nfcore_external_java_deps.jar ├── main.nf ├── modules.json ├── modules ├── local │ ├── bam_rename.nf │ ├── bambu.nf │ ├── bedtools_bamtobed.nf │ ├── bedtools_genomecov.nf │ ├── cutesv.nf │ ├── deepvariant.nf │ ├── deseq2.nf │ ├── dexseq.nf │ ├── get_chrom_sizes.nf │ ├── get_jaffal_ref.nf │ ├── get_nanolyse_fasta.nf │ ├── get_test_data.nf │ ├── graphmap2_align.nf │ ├── graphmap2_index.nf │ ├── gtf2bed.nf │ ├── jaffal.nf │ ├── m6anet_dataprep.nf │ ├── m6anet_inference.nf │ ├── medaka_variant.nf │ ├── minimap2_align.nf │ ├── minimap2_index.nf │ ├── multiqc.nf │ ├── nanopolish_index_eventalign.nf │ ├── pepper_margin_deepvariant.nf │ ├── qcat.nf │ ├── samplesheet_check.nf │ ├── samtools_sort_index.nf │ ├── samtools_view_bam.nf │ ├── sniffles.nf │ ├── stringtie2.nf │ ├── subread_featurecounts.nf │ ├── ucsc_bed12tobigbed.nf │ ├── ucsc_bedgraphtobigwig.nf │ ├── xpore_dataprep.nf │ └── xpore_diffmod.nf └── nf-core │ ├── bcftools │ └── sort │ │ ├── main.nf │ │ └── meta.yml │ ├── custom │ └── dumpsoftwareversions │ │ ├── main.nf │ │ ├── meta.yml │ │ └── templates │ │ └── dumpsoftwareversions.py │ ├── fastqc │ ├── main.nf │ └── meta.yml │ ├── multiqc │ ├── main.nf │ └── meta.yml │ ├── nanolyse │ ├── main.nf │ └── meta.yml │ ├── nanoplot │ ├── main.nf │ └── meta.yml │ ├── samtools │ ├── faidx │ │ ├── main.nf │ │ └── meta.yml │ ├── flagstat │ │ ├── main.nf │ │ └── meta.yml │ ├── idxstats │ │ ├── main.nf │ │ └── meta.yml │ ├── index │ │ ├── main.nf │ │ └── meta.yml │ ├── sort │ │ ├── main.nf │ │ └── meta.yml │ └── stats │ │ ├── main.nf │ │ └── meta.yml │ ├── stringtie │ └── merge │ │ ├── main.nf │ │ └── meta.yml │ ├── tabix │ ├── bgzip │ │ ├── main.nf │ │ └── meta.yml │ ├── bgziptabix │ │ ├── main.nf │ │ └── meta.yml │ └── tabix │ │ ├── main.nf │ │ └── meta.yml │ └── untar │ ├── main.nf │ └── meta.yml ├── nextflow.config ├── nextflow_schema.json ├── pyproject.toml ├── subworkflows ├── local │ ├── align_graphmap2.nf │ ├── align_minimap2.nf │ ├── bam_sort_index_samtools.nf │ ├── bedtools_ucsc_bigbed.nf │ ├── bedtools_ucsc_bigwig.nf │ ├── differential_deseq2_dexseq.nf │ ├── input_check.nf │ ├── prepare_genome.nf │ ├── qcfastq_nanoplot_fastqc.nf │ ├── quantify_stringtie_featurecounts.nf │ ├── rna_fusions_jaffal.nf │ ├── rna_modifications_xpore_m6anet.nf │ ├── short_variant_calling.nf │ └── 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