├── .dockerignore ├── .gitattributes ├── .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 ├── base.config ├── bin ├── deconcatenate.py ├── trim.py ├── workflow-glue └── workflow_glue │ ├── __init__.py │ ├── bokeh_plot.py │ ├── find_inserts.py │ ├── models │ ├── __init__.py │ └── common.py │ ├── report.py │ ├── report_utils │ └── report_utils.py │ ├── run_plannotate.py │ ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── test_deconcatenate.py │ ├── test_find_inserts.py │ ├── test_report.py │ └── test_run_plannotate.py │ ├── trim.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 ├── .gitkeep ├── OPTIONAL_FILE └── primers.tsv ├── 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 │ ├── canu_assembly.nf │ └── flye_assembly.nf ├── nextflow.config ├── nextflow_schema.json ├── output_definition.json └── test_data ├── .gitkeep ├── client_fields.json ├── cutsite_test.fasta ├── fastq-no-basecall-model └── barcode01 │ └── test1.fastq ├── insert_reference.fasta ├── other_reference.fasta ├── plasmid.bam ├── sample_sheet.txt ├── sample_sheet_cutsite.csv ├── sample_sheet_hosts.csv ├── sample_sheet_number.csv ├── test ├── barcode01 │ └── test1.fastq ├── barcode02 │ └── test2.fastq ├── barcode03 │ └── test3.fastq └── barcode04 │ └── .gitkeep ├── test_forward_full_ref.fasta ├── test_medaka_model.tar.gz ├── test_reverse_full_ref.fasta └── workflow_glue ├── deconcatenate ├── barcode01.fasta ├── barcode01_expected.fasta ├── barcode02.fasta ├── barcode02_expected.fasta ├── barcode03.fasta ├── barcode03_expected.fasta ├── barcode04.fasta ├── barcode04_expected.fasta ├── barcode05.fasta └── barcode05_expected.fasta ├── find_inserts ├── assemblies │ ├── barcode01.final.fasta │ ├── barcode02.final.fasta │ ├── barcode03.final.fasta │ └── barcode04.final.fasta ├── expected_df.csv ├── expected_insert │ ├── barcode01.insert.fasta │ ├── barcode01.insert.fasta.fai │ ├── barcode02.insert.fasta │ ├── barcode02.insert.fasta.fai │ ├── barcode03.insert.fasta │ ├── barcode03.insert.fasta.fai │ ├── barcode04.insert.fasta │ └── barcode04.insert.fasta.fai ├── insert_beds │ ├── internal_forward.bed │ ├── internal_reverse.bed │ ├── split_forward.bed │ └── split_reverse.bed └── primers │ ├── internal_forward.tsv │ ├── internal_reverse.tsv │ ├── split_forward.tsv │ └── split_reverse.tsv ├── report └── cut_sites.csv └── run_plannotate ├── barcode01.annotations.gbk └── barcode01.fasta /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epi2me-labs/wf-clone-validation/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/epi2me-labs/wf-clone-validation/HEAD/.github/ISSUE_TEMPLATE/bug_report.yml 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