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Viral genomics analysis pipelines
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Can viral-ngs detect virus integration? #1011

Open doeun99 opened 11 months ago

doeun99 commented 11 months ago

Hello :)

I have a question regarding viral-ngs and its capabilities for detecting virus integration and outputting the results to a text file. I tried to understand the explanation provided in the manual at https://viral-ngs.readthedocs.io/en/latest/, but as a beginner, I found it difficult to grasp the details of the result and virus integration.

Could you please confirm if viral-ngs can detect virus integration and output the results to a text file that includes chromosome and position information? Additionally, I would like to know if it's possible to utilize a pipeline using either cromwell or snakemake as described in sections 4 and 5 of the documentation.

For your reference, I cloned the viral-ngs repository from https://github.com/broadinstitute/viral-ngs.git and installed it using the command ". /easy-deploy-script/easy-deploy-viral-ngs.sh setup." Before executing viral-ngs pipeline, I reviewed the "issue (#749)" that recommends using WDL over snakemake. Thus, I referred to the the following link: https://github.com/broadinstitute/viral-ngs/blob/master/travis/tests-cromwell.sh.

thank you

I obtained the following log: on Jul 10 15:57:41 KST 2023 Executing * using Cromwell on local instance Error: Unknown argument 'assemble_denovo.wdl' Error: Unknown argument 'assemble_denovo_with_deplete_and_isnv_calling.wdl' Error: Unknown argument 'assemble_denovo_with_deplete.wdl' Error: Unknown argument 'assemble_denovo_with_isnv_calling.wdl' Error: Unknown argument 'assemble_refbased.wdl' Error: Unknown argument 'classify_kaiju.wdl' Error: Unknown argument 'classify_krakenuniq.wdl' Error: Unknown argument 'contigs.wdl' Error: Unknown argument 'coverage_table.wdl' Error: Unknown argument 'demux_metag.wdl' Error: Unknown argument 'demux_only.wdl' Error: Unknown argument 'demux_plus.wdl' Error: Unknown argument 'deplete_only.wdl' Error: Unknown argument 'fetch_annotations.wdl' Error: Unknown argument 'filter_classified_bam_to_taxa.wdl' Error: Unknown argument 'genbank.wdl' Error: Unknown argument 'isnvs_merge_to_vcf.wdl' Error: Unknown argument 'isnvs_one_sample.wdl' Error: Unknown argument 'mafft.wdl' Error: Unknown argument 'merge_bams.wdl' Error: Unknown argument 'read_utils.wdl' Error: Unknown argument 'scaffold_and_refine.wdl' Error: Unknown argument 'spikein.wdl' Error: Unknown argument 'tasks_assembly.wdl' Error: Unknown argument 'tasks_demux.wdl' Error: Unknown argument 'tasks_interhost.wdl' Error: Unknown argument 'tasks_intrahost.wdl' Error: Unknown argument 'tasks_metagenomics.wdl' Error: Unknown argument 'tasks_ncbi.wdl' Error: Unknown argument 'tasks_read_utils.wdl' Error: Unknown argument 'tasks_reports.wdl' Error: Unknown argument 'tasks_taxon_filter.wdl' Try --help for more information. cromwell 40 Usage: java -jar /path/to/cromwell.jar [server|run|submit] [options] ...

--help Cromwell - Workflow Execution Engine --version Command: server Starts a web server on port 8000. See the web server documentation for more details about the API endpoints. Command: run [options] workflow-source Run the workflow and print out the outputs in JSON format. workflow-source Workflow source file or workflow url. --workflow-root Workflow root. -i, --inputs Workflow inputs file. -o, --options Workflow options file. -t, --type Workflow type. -v, --type-version Workflow type version. -l, --labels Workflow labels file. -p, --imports A directory or zipfile to search for workflow imports. -m, --metadata-output An optional directory path to output metadata. Command: submit [options] workflow-source Submit the workflow to a Cromwell server. workflow-source Workflow source file or workflow url. --workflow-root Workflow root. -i, --inputs Workflow inputs file. -o, --options Workflow options file. -t, --type Workflow type. -v, --type-version Workflow type version. -l, --labels Workflow labels file. -p, --imports A directory or zipfile to search for workflow imports. -h, --host Cromwell server URL. /home/kde/PROJECTS/VirusIntegrationTools/download/viral-ngs/travis Mon Jul 10 15:57:41 KST 2023 note: there is no testing of output correctness yet...

dpark01 commented 11 months ago

Hi @doeun99 , Sorry I was out of office in Korea for the past 3 weeks and am catching up on these items.

viral-ngs is not designed to detect viral integration--while there may be tools out there that exist for this, we don't have any of those tools in this toolsuite.

Most of the functionality in viral-ngs for viral assembly, metagenomics, etc, are currently being maintained in the viral-pipelines repository as WDL pipelines. The documentation there will be more up to date and easier to use if you want to use any of those tools. But we don't have anything for integration detection.