pre_aocd_bwa channel, which has the sample name, cleaned fastq reads file and consensus fasta file
This process (actually 2 processes) executes bwa and samtools calls to calculate the average coverage depth per sample
a data channel which has the sample name and the calculated average coverage depth value
seqyclean process and ivar_consensus process
There are actually 2 processes (coverage_depth_bwa, and coverage_depth_samtools). This is due to:
- One process can only use one container image, but we need to use both bwa and samtools tools
- Utilize parallelisation by splitting the whole process into 2 sub-processes.
Rong Jin