💠Pipeline Logic
Last updated
Last updated
| Step | Module/Script | Run |
|---|---|---|
QC | trimmomatic | Always |
Primer trimming (on FASTQ) | trimmomatic | If assembly is to run |
Remove off-target reads | DRAGEN | If checked in Input Form |
Assembly | MEGAHIT | If reference FASTA and BED files imply more than one genome as reference |
Contig clustering | CD-HIT | If assembly ran |
Reference selection | custom script | If assembly ran, otherwise input reference database is used as is |
Map/Align | DRAGEN | If at least one reference sequence is generated |
Post-facto primer trimming (on BAM) | custom script | If Map/Align ran and primer set exists |
Sample filtering based on amplicon coverage | custom script | If Map/Align ran and primer set exists |
Variant calling | DRAGEN | If Map/Align ran and sample passed filter above |
Consensus sequence generation | custom script | If Map/Align ran and sample passed filter above |
| Status | Level | Outcome |
|---|---|---|
Completed successfully | Pipeline | Exit with all applicable output files |
Custom files are not formatted correctly | Pipeline | Exit early with error |
No remaining reads after preprocessing | Sample | Exit early with a report of read counts |
No contig generated | Sample | Exit early with a report of read counts |
No reference found after assembly | Sample | Exit early with a report of read counts and contig FASTA |
None of the primers provided in custom primer definition file align to selected reference sequences | Sample | Skip post-factor primer trimming and sample filtering based on amplicon coverage for this sample |
Insufficient amplicon coverage | Sample | Exit early before variant calling and consensus sequence generation |
