LongTREC nextflow training

Practice Session: Create a nextflow pipeline using minimap2

This repository serves as a (very basic) solution to the task of creating a nextflow pipeline to run minimap2. Note that there are many ways in which this can be improved such as:

• providing different parameters (beyond basic differentiation of data type)
• accommodating different input formats (e.g. .fq.gz, PacBio .bam)
• accommodating different output formats (e.g. .bam)
• including indexing

etc.

Note that the example data in /data and /reference is taken from IsoQuant