.gitignore
LICENSE
MANIFEST.in
NOTICE
README.md
conftest.py
mkdocs.yml
pyproject.toml
setup.py
.github/dependabot.yml
.github/actions/python_build/action.yml
.github/workflows/notice.yml
.github/workflows/publish.yml
cicd/gitlab/dot.gitlab-ci.yml
cicd/gitlab/parts/ci.gitlab-ci.yml
cicd/gitlab/parts/debug.gitlab-ci.yml
cicd/gitlab/parts/dockerbuild.genomio.gitlab-ci.yml
cicd/gitlab/parts/flatfile.gitlab-ci.yml
cicd/gitlab/parts/license.gitlab-ci.yml
cicd/gitlab/parts/perl.gitlab-ci.yml
cicd/gitlab/parts/python.gitlab-ci.yml
cicd/runtime/.gitignore
cicd/scripts/check_flatfile.py
cicd/scripts/check_license.py
cicd/templates/license_header.tpl
cicd/templates/notice.tpl
config/external_db_map/default.txt
config/external_db_map/minimal.txt
config/gff_metaparser/metaparser.conf
config/gff_metaparser/valid_structures.conf
config/gff_metaparser/metaparser/brc4.patch
config/gff_metaparser/metaparser/cds_with_parent_id.patch
config/gff_metaparser/metaparser/cncb_hgdc.conf
config/gff_metaparser/metaparser/flybase.conf
config/gff_metaparser/metaparser/ids2display.conf
config/gff_metaparser/metaparser/mgnify_prodig.conf
config/gff_metaparser/metaparser/no_protein_id.patch
config/gff_metaparser/metaparser/noxref.patch
config/gff_metaparser/metaparser/old_refseq_brc4.conf
config/gff_metaparser/metaparser/regions_no_syns.patch
config/gff_metaparser/metaparser/xref2gene.patch
config/gff_metaparser/valid_structures/test_pre_mirna.conf
config/gff_metaparser/valid_structures/test_sub.conf
containers/docker/genomio/Dockerfile
data/test/exon_cds_duplicated_ids_test.gff3
data/test/gene_cds_test.gff3
data/test/pre_mirna_test.gff3
data/test/sub_rule_test.gff3
data/test/circular_transspliced_feature/mt.fna
data/test/circular_transspliced_feature/pep.faa
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data/test/modules/download_asm_data/output/GCA_017607445.1_ASM1760744v1_assembly_report.txt
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data/test/modules/download_asm_data/output/GCA_017607445.1_ASM1760744v1_protein.faa.gz
data/test/modules/download_genbank/output/output.gb
data/test/pipelines/dumper/db_factory_dbs.json
data/test/pipelines/dumper/dump_files/downloaded_ncbi_stats.json
data/test/pipelines/dumper/dump_files/dumped_core_stats.json
data/test/pipelines/dumper/dump_files/dumped_dna.fasta
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data/test/pipelines/dumper/dump_files/dumped_pep.fasta
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docs/BRC4_genome_compare_conf.md
docs/BRC4_genome_loader.md
docs/cicd_gitlab.md
docs/code_of_conduct.md
docs/genome_prepare.md
docs/index.md
docs/install.md
docs/nextflow.md
docs/pipelines.md
docs/trf_split_run.md
docs/usage.md
docs/img/ensembl-logo.png
docs/scripts/gen_ref_pages.py
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pipelines/nextflow/README.md
pipelines/nextflow/log_template.md
pipelines/nextflow/template_meta.yml
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pipelines/nextflow/modules/database/db_factory.nf
pipelines/nextflow/modules/database/dump_db.nf
pipelines/nextflow/modules/download/datasets_genome_meta.nf
pipelines/nextflow/modules/download/download_asm_data.nf
pipelines/nextflow/modules/download/download_genbank.nf
pipelines/nextflow/modules/events/dump_events.nf
pipelines/nextflow/modules/fasta/dump_fasta_dna.nf
pipelines/nextflow/modules/fasta/dump_fasta_peptides.nf
pipelines/nextflow/modules/fasta/process_fasta_data.nf
pipelines/nextflow/modules/files/publish_output.nf
pipelines/nextflow/modules/files/publish_output_dump.nf
pipelines/nextflow/modules/genbank/extract_from_gb.nf
pipelines/nextflow/modules/genome_metadata/accession_metadata.nf
pipelines/nextflow/modules/genome_metadata/amend_genome_data.nf
pipelines/nextflow/modules/genome_metadata/dump_genome_meta.nf
pipelines/nextflow/modules/genome_metadata/prepare_genome_metadata.nf
pipelines/nextflow/modules/genome_stats/compare_genome_stats.nf
pipelines/nextflow/modules/genome_stats/dump_genome_stats.nf
pipelines/nextflow/modules/gff3/dump_gff3.nf
pipelines/nextflow/modules/gff3/gff3_validation.nf
pipelines/nextflow/modules/gff3/process_gff3.nf
pipelines/nextflow/modules/gff3/unpack_gff3.nf
pipelines/nextflow/modules/manifest/integrity.nf
pipelines/nextflow/modules/manifest/manifest_maker.nf
pipelines/nextflow/modules/manifest/manifest_stats.nf
pipelines/nextflow/modules/schema/check_json_schema.nf
pipelines/nextflow/modules/schema/check_json_schema_db.nf
pipelines/nextflow/modules/schema/json_schema_factory.nf
pipelines/nextflow/modules/seq_region/dump_agp.nf
pipelines/nextflow/modules/seq_region/dump_seq_attrib.nf
pipelines/nextflow/modules/seq_region/dump_seq_regions.nf
pipelines/nextflow/modules/seq_region/process_seq_region.nf
pipelines/nextflow/modules/utils/utils.nf
pipelines/nextflow/subworkflows/yaml-schema.json
pipelines/nextflow/subworkflows/additional_seq_prepare/main.nf
pipelines/nextflow/subworkflows/additional_seq_prepare/meta.yml
pipelines/nextflow/subworkflows/dump_files/main.nf
pipelines/nextflow/subworkflows/dump_sql/main.nf
pipelines/nextflow/subworkflows/genome_prepare/main.nf
pipelines/nextflow/subworkflows/genome_prepare/meta.yml
pipelines/nextflow/tests/workflows/nextflow_test.config
pipelines/nextflow/tests/workflows/test_addition_prepare.yml
pipelines/nextflow/tests/workflows/test_dumper_files.yml
pipelines/nextflow/tests/workflows/test_dumper_sql.yml
pipelines/nextflow/tests/workflows/test_genome_prepare.yml
pipelines/nextflow/tests/workflows/test_genome_prepare_brc.yml
pipelines/nextflow/workflows/nextflow.config
pipelines/nextflow/workflows/additional_seq_prepare/main.nf
pipelines/nextflow/workflows/additional_seq_prepare/nextflow.config
pipelines/nextflow/workflows/additional_seq_prepare/nextflow_schema.json
pipelines/nextflow/workflows/conf/additional_seq_prepare-genomio.config
pipelines/nextflow/workflows/conf/dumper_pipeline-ensembllegacy.config
pipelines/nextflow/workflows/conf/dumper_pipeline-genomio.config
pipelines/nextflow/workflows/conf/genome_prepare-genomio.config
pipelines/nextflow/workflows/dumper_pipeline/README.md
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pipelines/nextflow/workflows/dumper_pipeline/nextflow.config
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scripts/README.md
scripts/get_dna_fasta_for.pl
scripts/load_fann.pl
scripts/trf_split_run.bash
scripts/gff_metaparser/gen_meta_conf.py
scripts/gff_metaparser/gff3_meta_parse.py
scripts/gff_metaparser/gff_stats.py
scripts/gff_metaparser/genmetaconf/__init__.py
scripts/gff_metaparser/genmetaconf/manifest.py
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scripts/gff_metaparser/gffstruct/rules/unseen.py
scripts/gff_metaparser/gffstruct/rules/valid.py
scripts/stable_id_alloc/allocate_stable_ids.pl
scripts/stable_id_alloc/osid_add_organisms.py
scripts/stable_id_alloc/osid_check_organisms.py
src/containers/example.Dockerfile
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src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/BRC4_genome_loader_conf.pm
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/LoadGFF3Batch_conf.pm
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/LoadGFF3_conf.pm
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/README.md
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/gff3.ignore
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src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/DumpFastaDNA.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/DumpJsonBase.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/DumpSeqRegionJson.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/GetMetaValue.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/ServerFromRegistry.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/AddSynonyms.pm
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src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/ApplySeqEdits.pm
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src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/ConstructFilenames.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/DeleteGenes.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/EmailReport.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/FixModels.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/LoadGFF3.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/ReportSeqEdits.pm
src/python/ensembl/brc4/__init__.py
src/python/ensembl/brc4/runnable/__init__.py
src/python/ensembl/brc4/runnable/compare_fasta.py
src/python/ensembl/brc4/runnable/compare_report.py
src/python/ensembl/brc4/runnable/fill_metadata.py
src/python/ensembl/brc4/runnable/json_schema_factory.py
src/python/ensembl/brc4/runnable/load_sequence_data.py
src/python/ensembl/brc4/runnable/prepare_genome.py
src/python/ensembl/brc4/runnable/seqregion_parser.py
src/python/ensembl/io/genomio/__init__.py
src/python/ensembl/io/genomio/annotation/__init__.py
src/python/ensembl/io/genomio/annotation/update_description.py
src/python/ensembl/io/genomio/assembly/__init__.py
src/python/ensembl/io/genomio/assembly/download.py
src/python/ensembl/io/genomio/assembly/status.py
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src/python/ensembl/io/genomio/data/external_db_map/__init__.py
src/python/ensembl/io/genomio/data/external_db_map/default.txt
src/python/ensembl/io/genomio/data/external_db_map/minimal.txt
src/python/ensembl/io/genomio/data/gff3/__init__.py
src/python/ensembl/io/genomio/data/gff3/biotypes.json
src/python/ensembl/io/genomio/data/schemas/__init__.py
src/python/ensembl/io/genomio/data/schemas/functional_annotation.json
src/python/ensembl/io/genomio/data/schemas/genome.json
src/python/ensembl/io/genomio/data/schemas/load_features.json
src/python/ensembl/io/genomio/data/schemas/manifest.json
src/python/ensembl/io/genomio/data/schemas/seq_attrib.json
src/python/ensembl/io/genomio/data/schemas/seq_region.json
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src/python/ensembl/io/genomio/database/meta_getter.py
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src/python/ensembl/io/genomio/features/combine_json.py
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src/python/ensembl/io/genomio/genbank/__init__.py
src/python/ensembl/io/genomio/genbank/download.py
src/python/ensembl/io/genomio/genbank/extract_data.py
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