├── .dockerignore ├── .github └── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ ├── feature_request.yml │ └── question.yml ├── .gitignore ├── .gitlab-ci.yml ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── bin ├── get_nexclade_data.sh ├── run_artic.sh ├── workflow-glue └── workflow_glue │ ├── __init__.py │ ├── combine_genotype_summaries.py │ ├── genotype_summary.py │ ├── models │ ├── __init__.py │ └── common.py │ ├── report.py │ ├── report_error.py │ ├── seq_summary.py │ ├── tests │ ├── __init__.py │ └── test_test.py │ ├── util.py │ └── wfg_helpers │ ├── __init__.py │ ├── check_bam_headers_in_dir.py │ ├── check_sample_sheet.py │ ├── check_xam_index.py │ ├── configure_igv.py │ ├── get_max_depth_locus.py │ └── reheader_samstream.py ├── data ├── OPTIONAL_FILE ├── nextclade │ └── datasets │ │ └── sarscov2 │ │ └── 2024-02-16T04-00-32Z │ │ ├── CHANGELOG.md │ │ ├── README.md │ │ ├── genome_annotation.gff3 │ │ ├── pathogen.json │ │ ├── reference.fasta │ │ ├── sequences.fasta │ │ └── tree.json └── primer_schemes │ └── SARS-CoV-2 │ ├── ARTIC │ ├── V1 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ ├── V2 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ ├── V3 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ ├── V4.1 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ ├── V4 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ └── V5.3.2 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ ├── Midnight-IDT │ ├── V1 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ └── V2 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ ├── Midnight-ONT │ ├── V1 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ ├── V2 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ └── V3 │ │ ├── SARS-CoV-2.reference.fasta │ │ ├── SARS-CoV-2.reference.fasta.fai │ │ └── SARS-CoV-2.scheme.bed │ └── NEB-VarSkip │ ├── v1a-long │ ├── SARS-CoV-2.reference.fasta │ ├── SARS-CoV-2.reference.fasta.fai │ └── SARS-CoV-2.scheme.bed │ ├── v1a │ ├── SARS-CoV-2.reference.fasta │ ├── SARS-CoV-2.reference.fasta.fai │ └── SARS-CoV-2.scheme.bed │ ├── v2 │ ├── SARS-CoV-2.reference.fasta │ ├── SARS-CoV-2.reference.fasta.fai │ └── SARS-CoV-2.scheme.bed │ └── v2b │ ├── SARS-CoV-2.reference.fasta │ ├── SARS-CoV-2.reference.fasta.fai │ └── SARS-CoV-2.scheme.bed ├── docs ├── 01_brief_description.md ├── 02_introduction.md ├── 03_compute_requirements.md ├── 04_install_and_run.md ├── 05_related_protocols.md ├── 06_input_example.md ├── 06_input_parameters.md ├── 07_outputs.md ├── 08_pipeline_overview.md ├── 09_troubleshooting.md ├── 10_FAQ.md └── 11_other.md ├── lib ├── ArgumentParser.groovy ├── CWUtil.groovy ├── NfcoreSchema.groovy ├── NfcoreTemplate.groovy ├── Pinguscript.groovy ├── WorkflowMain.groovy ├── common.nf ├── ingress.nf └── nfcore_external_java_deps.jar ├── main.nf ├── nextflow.config ├── nextflow_schema.json ├── output_definition.json └── test_data ├── .gitkeep ├── fastq-no-basecall-model └── barcode01 │ └── reads.fq.gz ├── fastq ├── barcode01 │ └── fastq_runid_0000000000000000000000000000000000000000_0_0.fastq.gz ├── barcode02 │ └── fastq_runid_0000000000000000000000000000000000000000_0_0.fastq.gz ├── barcode13 │ └── .gitkeep └── barcode99 │ └── test.fastq.gz └── sample_sheet.csv /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epi2me-labs/wf-artic/HEAD/.dockerignore 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