├── .coveragerc ├── .dockstore.yml ├── .gitattributes ├── .github └── workflows │ └── build.yml ├── .gitignore ├── .readthedocs.yml ├── CLAUDE.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── conf.py ├── description.rst ├── index.rst ├── ncbi_submission.rst ├── pipes-wdl.rst ├── requirements.txt ├── rulegraph.png ├── viral-ngs-overview.png └── workflows.rst ├── github_actions_ci ├── build-docs.sh ├── build-dx.sh ├── check-wdl-runtimes.sh ├── dockstoreyml.sh ├── install-pip-docs.sh ├── install-wdl.sh ├── list-docker-tags.sh ├── relative-wdl-paths.sh ├── tests-cromwell.sh ├── tests-dx.sh ├── tests-miniwdl.sh ├── validate-wdl-womtool.sh └── version-wdl-runtimes.sh ├── pipes ├── WDL │ ├── tasks │ │ ├── tasks_16S_amplicon.wdl │ │ ├── tasks_assembly.wdl │ │ ├── tasks_demux.wdl │ │ ├── tasks_interhost.wdl │ │ ├── tasks_intrahost.wdl │ │ ├── tasks_megablast.wdl │ │ ├── tasks_metagenomics.wdl │ │ ├── tasks_ncbi.wdl │ │ ├── tasks_ncbi_tools.wdl │ │ ├── tasks_nextstrain.wdl │ │ ├── tasks_read_utils.wdl │ │ ├── tasks_reports.wdl │ │ ├── tasks_sarscov2.wdl │ │ ├── tasks_taxon_filter.wdl │ │ ├── tasks_terra.wdl │ │ └── tasks_utils.wdl │ └── workflows │ │ ├── align_and_count.wdl │ │ ├── align_and_count_multiple_report.wdl │ │ ├── align_and_plot.wdl │ │ ├── assemble_denovo.wdl │ │ ├── assemble_denovo_metagenomic.wdl │ │ ├── assemble_refbased.wdl │ │ ├── augur_export_only.wdl │ │ ├── augur_from_assemblies.wdl │ │ ├── augur_from_beast_mcc.wdl │ │ ├── augur_from_mltree.wdl │ │ ├── augur_from_msa.wdl │ │ ├── augur_from_msa_with_subsampler.wdl │ │ ├── bam_to_qiime.wdl │ │ ├── bams_multiqc.wdl │ │ ├── beast_gpu.wdl │ │ ├── blastoff.wdl │ │ ├── calc_bam_read_depths.wdl │ │ ├── classify_kaiju.wdl │ │ ├── classify_kraken2.wdl │ │ ├── classify_krakenuniq.wdl │ │ ├── classify_multi.wdl │ │ ├── classify_qiime2_multi.wdl │ │ ├── classify_single.wdl │ │ ├── coverage_table.wdl │ │ ├── create_enterics_qc_viz.wdl │ │ ├── create_enterics_qc_viz_general.wdl │ │ ├── demux_deplete.wdl │ │ ├── demux_metadata_only.wdl │ │ ├── demux_only.wdl │ │ ├── demux_plus.wdl │ │ ├── deplete_only.wdl │ │ ├── detect_cross_contamination.wdl │ │ ├── detect_cross_contamination_precalled_vcfs.wdl │ │ ├── diff_genome_sets.wdl │ │ ├── downsample.wdl │ │ ├── dump_gcloud_env_info.wdl │ │ ├── fastq_to_ubam.wdl │ │ ├── fetch_annotations.wdl │ │ ├── fetch_sra_to_bam.wdl │ │ ├── filter_classified_bam_to_taxa.wdl │ │ ├── filter_sequences.wdl │ │ ├── find_illumina_files.wdl │ │ ├── genbank_gather.wdl │ │ ├── genbank_single.wdl │ │ ├── isnvs_lofreq.wdl │ │ ├── isnvs_merge_to_vcf.wdl │ │ ├── isnvs_one_sample.wdl │ │ ├── kraken2_build.wdl │ │ ├── load_illumina_fastqs.wdl │ │ ├── load_illumina_fastqs_deplete.wdl │ │ ├── mafft.wdl │ │ ├── mafft_and_snp.wdl │ │ ├── mafft_and_snp_annotated.wdl │ │ ├── mafft_and_trim.wdl │ │ ├── megablast_chunk.wdl │ │ ├── merge_bams.wdl │ │ ├── merge_metagenomics.wdl │ │ ├── merge_tar_chunks.wdl │ │ ├── merge_vcfs.wdl │ │ ├── merge_vcfs_and_annotate.wdl │ │ ├── metagenomic_denovo.wdl │ │ ├── multiqc_only.wdl │ │ ├── nextclade_single.wdl │ │ ├── pairwise_distances.wdl │ │ ├── populate_library_and_sample_tables_from_flowcell.wdl │ │ ├── reconstruct_from_alignments.wdl │ │ ├── sarscov2_batch_relineage.wdl │ │ ├── sarscov2_biosample_load.wdl │ │ ├── sarscov2_data_release.wdl │ │ ├── sarscov2_genbank.wdl │ │ ├── sarscov2_genbank_ingest.wdl │ │ ├── sarscov2_gisaid_ingest.wdl │ │ ├── sarscov2_illumina_full.wdl │ │ ├── sarscov2_lineages.wdl │ │ ├── sarscov2_nextclade_multi.wdl │ │ ├── sarscov2_nextstrain.wdl │ │ ├── sarscov2_nextstrain_aligned_input.wdl │ │ ├── sarscov2_sequencing_reports.wdl │ │ ├── sarscov2_sra_to_genbank.wdl │ │ ├── scaffold_and_refine.wdl │ │ ├── scaffold_and_refine_multitaxa.wdl │ │ ├── simulate_illumina_reads.wdl │ │ ├── submit_biosample.wdl │ │ ├── submit_genbank.wdl │ │ ├── submit_sra.wdl │ │ ├── subsample_by_casecounts.wdl │ │ ├── subsample_by_metadata.wdl │ │ ├── subsample_by_metadata_with_focal.wdl │ │ ├── terra_table_to_tsv.wdl │ │ ├── terra_tsv_to_table.wdl │ │ ├── terra_update_assemblies.wdl │ │ ├── trimal.wdl │ │ └── unpack_archive_to_bucket.wdl ├── cromwell │ ├── cromwell.gcid-viral-seq.conf │ ├── cromwell.local-github_actions.conf │ └── cromwell.local-travis.conf └── dnax │ ├── dx-defaults-assemble_denovo.json │ ├── dx-defaults-classify_kaiju.json │ ├── dx-defaults-classify_kraken2.json │ ├── dx-defaults-classify_krakenuniq.json │ ├── dx-defaults-classify_multi.json │ ├── dx-defaults-contigs.json │ ├── dx-defaults-demux_metag.json │ ├── dx-defaults-demux_plus.json │ ├── dx-defaults-deplete_only.json │ ├── dx-defaults-filter_classified_bam_to_taxa.json │ ├── dx-extras.json │ └── dx-launcher │ ├── .gitignore │ ├── README.md │ ├── consolidate_run_tarballs.yml │ ├── demux_launcher.yml │ └── dx-yml-build ├── requirements-modules.txt └── test └── input ├── 5kb_human_from_chr6.fasta ├── G5012.3.fasta ├── G5012.3.mini.bam ├── G5012.3.subset.bam ├── G5012.3.testreads.bam ├── LASV_NGA_2018_0026.fasta ├── LASV_NGA_2018_0097.fasta ├── LASV_NGA_2018_0541.fasta ├── MA_MGH_00003.fasta ├── MA_MGH_00004.fasta ├── MA_MGH_00005.fasta ├── TestSplitcodeDemuxFastqs ├── RunInfo.xml ├── SampleSheet.csv ├── TestPool1_S1_L001_R1_001.fastq.gz ├── TestPool1_S1_L001_R2_001.fastq.gz ├── TestPool3_S3_L001_R1_001.fastq.gz ├── TestPool3_S3_L001_R2_001.fastq.gz ├── biosample_map.tsv ├── sample_rename_map.tsv └── samples_3bc.tsv ├── WDL ├── cromwell-local │ ├── test_inputs-assemble_refbased-local.json │ ├── test_inputs-augur_from_assemblies-local.json │ ├── test_inputs-classify_kraken2-local.json │ ├── test_inputs-fastq_to_ubam-local.json │ ├── test_inputs-load_illumina_fastqs-local.json │ ├── test_inputs-load_illumina_fastqs_deplete-local.json │ ├── test_inputs-qiime_import_bam-local.json │ ├── test_outputs-load_illumina_fastqs-local.json │ └── test_outputs-load_illumina_fastqs_deplete-local.json ├── miniwdl-local │ ├── test_inputs-align_and_plot-local.json │ ├── test_inputs-assemble_denovo-local.json │ ├── test_inputs-assemble_refbased-local.json │ ├── test_inputs-augur_from_assemblies-local.json │ ├── test_inputs-augur_from_beast_mcc-local.json │ ├── test_inputs-classify_kraken2-local.json │ ├── test_inputs-fastq_to_ubam-local.json │ ├── test_inputs-genbank_single-local.json │ ├── test_inputs-load_illumina_fastqs-local.json │ ├── test_inputs-load_illumina_fastqs_deplete-local.json │ ├── test_inputs-qiime_import_bam-local.json │ ├── test_inputs-simulate_illumina_reads-local.json │ ├── test_outputs-assemble_denovo-local.json │ ├── test_outputs-assemble_refbased-local.json │ ├── test_outputs-load_illumina_fastqs-local.json │ ├── test_outputs-load_illumina_fastqs_deplete-local.json │ ├── test_outputs-sarscov2_lineages-local.json │ ├── test_task_inputs-get_illumina_run_metadata-local.json │ └── test_task_inputs-group_fastq_pairs-local.json ├── test_inputs-align_and_plot-local.json ├── test_inputs-assemble_denovo-dnanexus.dx.json ├── test_inputs-assemble_denovo-local.json ├── test_inputs-assemble_refbased-local.json ├── test_inputs-augur_from_assemblies-local.json ├── test_inputs-augur_from_beast_mcc-local.json ├── test_inputs-beast_gpu-local_nonauto.json ├── test_inputs-classify_kraken2-local.json ├── test_inputs-classify_multi-dnanexus.dx.json ├── test_inputs-demux_plus-dnanexus.dx.json ├── test_inputs-fastq_to_ubam-local.json ├── test_inputs-genbank_single-local.json ├── test_inputs-load_illumina_fastqs-local.json ├── test_inputs-load_illumina_fastqs_deplete-local.json ├── test_inputs-qiime_import_bam-local.json ├── test_inputs-sarscov2_lineages-local.json ├── test_outputs-assemble_denovo-local.json ├── test_outputs-assemble_refbased-local.json ├── test_outputs-load_illumina_fastqs-local.json ├── test_outputs-load_illumina_fastqs_deplete-local.json └── test_outputs-sarscov2_lineages-local.json ├── beast-lasv.tree ├── beast-mers-auspice_config.json ├── beast-mers-mcc.tree ├── beast-simple-ebov-20k.xml ├── clipDb.fasta ├── ebov-makona.fasta ├── genbank ├── KM821997.1.fasta ├── KM821997.1.tbl ├── KM821998.1.fasta ├── KM821998.1.tbl ├── LASV_NGA_2018_0026-aligned.bam ├── MN908947.3.fasta ├── MN908947.3.tbl ├── author_template.sbt.j2 ├── authors-nga_lasv.sbt ├── biosample-attributes-lasv.txt ├── biosample-map-lasv-2018-RUN1.txt ├── coverage-ma_mgh.txt ├── coverage_report-RUN1-new_names.txt ├── coverage_report-RUN1-workflow.txt ├── default_sbt_values.yaml ├── expected │ ├── LASV_NGA_2018_0026-1.cmt │ ├── LASV_NGA_2018_0026-1.fsa │ ├── LASV_NGA_2018_0026-1.gbf │ ├── LASV_NGA_2018_0026-1.sqn │ ├── LASV_NGA_2018_0026-1.src │ ├── LASV_NGA_2018_0026-1.tbl │ ├── LASV_NGA_2018_0026-1.val │ ├── LASV_NGA_2018_0026-2.cmt │ ├── LASV_NGA_2018_0026-2.fsa │ ├── LASV_NGA_2018_0026-2.gbf │ ├── LASV_NGA_2018_0026-2.sqn │ ├── LASV_NGA_2018_0026-2.src │ ├── LASV_NGA_2018_0026-2.tbl │ ├── LASV_NGA_2018_0026-2.val │ ├── LASV_NGA_2018_0097-1.cmt │ ├── LASV_NGA_2018_0097-1.fsa │ ├── LASV_NGA_2018_0097-1.gbf │ ├── 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