├── .dockerignore ├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ ├── feature_request.yml │ └── question.yml └── workflows │ └── issue-autoreply.yml ├── .gitignore ├── .gitlab-ci.yml ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── bin ├── create_pairs_report.py ├── workflow-glue └── workflow_glue │ ├── __init__.py │ ├── models │ ├── __init__.py │ └── common.py │ ├── report.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 ├── 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 ├── modules └── local │ ├── 4dn.nf │ ├── common.nf │ └── pore-c.nf ├── nextflow.config ├── nextflow_schema.json ├── output_definition.json ├── subworkflows └── local │ └── prepare_genome.nf └── test_data ├── bams ├── barcode01 │ └── porec_test.concatemers.bam └── barcode02 │ └── porec_test.concatemers.bam ├── bams_dir ├── shard_0001.bam ├── shard_0002.bam ├── shard_0003.bam └── shard_0004.bam ├── porec_test.concatemers.bam ├── porec_test.concatemers.fastq ├── porec_test.fasta ├── porec_test.fasta.fai ├── porec_test.monomer.fastq ├── porec_test.params.json ├── porec_test.phased_variants.vcf.gz ├── porec_test.phased_variants.vcf.gz.tbi ├── porec_test_no_index.phased_variants.vcf.gz ├── sample_sheet.csv ├── sample_sheet_cutter.csv ├── sample_sheet_no_tbi.csv ├── sample_sheet_no_vcf.csv └── tests.pairs.stats.txt /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epi2me-labs/wf-pore-c/HEAD/.dockerignore -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epi2me-labs/wf-pore-c/HEAD/.editorconfig -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epi2me-labs/wf-pore-c/HEAD/.github/ISSUE_TEMPLATE/bug_report.yml -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/config.yml: 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