This repo contains all our mpox related workflows.
Currently we use the XGen tiled amplicon primer scheme for WGS. We then perform genome assembly using Theiagen Genomic's PHB wf_theiacov_illumina_pe.wdl on the Terra platform. Following assembly we transfer the resutls and intermediate files to our GCP buckets using the TheaiCov_mpox_transfer.wdl.
This wdl workflow transfers the result files and intermediate files from the wf_theiacov_illumina_pe.wdl workflow to our bucket.
| Input Variable | description |
|---|---|
| sample_name | column with the list of sample names (e.g. the entity:data_name_id) |
| transfer_bucket_path | user defined google bucket for where the files will be transferred to, string |
| aligned_bam | bam files |
| assembly_fasta | consensus fasteas |
| consesnus_stats | |
| ivar_tsv | vcf file output from ivar |
| ivar_vcf | vcf file ouptut from ivar |
| kraken_report | kraken report output from kraken |
| kraken_report_dehosted | kraken report output from kraken |
| nextclade_json | nextclade json file output from nextclade |
| nextclade_tsv | nextclade file output from nextclade |
| read1_dehosted | scrubbed fastq file of human read data |
| read2_dehosted | scrubbed fastq file of human read data |