| 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
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