In places where reads can be processed as paired- or single-end reads, they need to be processed agnostic of whether they are Illumina/Nanopore/PacBio/etc. reads.
Added Features
Additional processes
To implement the --interleaved flag, SeqTK (Docker image), will need to implement a deinterleaving process.
Added (and Modified) parameters
--platform
Maintains its function and purpose
--paired
type: flag
default: (params.platform == "illumina")
Whether the reads are paired-end
--interleaved
type: flag
default: false
Use one file per sample with read ends alternating (interleaved reads file)
--ont
This parameter will be removed
--pe
This parameter might be kept as an alias for --paired for backwards compatability
More Info
Context
The pipeline was unable to process Single-end Illumina reads. The way reads are processed now is not reflective of reality.
Alternatives
The only alternative currently is to run the reads using --platform ont.
Possible implementation
[ ] Add the --paired flag and remove the --ont (possibly the --pe) flag
Summary
In places where reads can be processed as paired- or single-end reads, they need to be processed agnostic of whether they are Illumina/Nanopore/PacBio/etc. reads.
Added Features
Additional processes
To implement the
--interleavedflag, SeqTK (Docker image), will need to implement a deinterleaving process.Added (and Modified) parameters
--platform--pairedflag(params.platform == "illumina")--interleavedflagfalse--ont--pe--pairedfor backwards compatabilityMore Info
Context
The pipeline was unable to process Single-end Illumina reads. The way reads are processed now is not reflective of reality.
Alternatives
The only alternative currently is to run the reads using
--platform ont.Possible implementation
--pairedflag and remove the--ont(possibly the--pe) flag--pairedflag--platformflag--interleavedflag