minimap2 align with increasing index size

[yumisims]

Description of feature

potentially would replace the current split-prefix to tackle genome size over 4GB.

[weaglesBio]

Yumi's Testing -I mode 5h 50 min runtime, 45 GB RAM --split-prefix mode 19h 30 min runtime, 29 GB RAM. I can see in the log file how the target genome was virtually split into three chunks, each under 4 Gbp, and reads were aligned to each chunk. That’s why it was about 3 times as slow as the -I mod

[weaglesBio]

Need to implement in

• [ ] long read coverage subworkflow
• [ ] gene alignment for cds/cdna/rna

Task: Change the split-prefix to minimap2 -ax splice --cs=short -t 6 -I12g for cds, cdna and rna mapping (edited) 12g can be other value parse as argument

Look at dp24 organellar

[yumisims]

completed