Not going to lie, my head hurts when I read the NextFlow documentation (No dig on the documentation, I think my head is losing its processing capacity lol).
I had written a pipeline in Bash, essentially iterates over a text file containing full paths of R1 and R2 reads, followed by a series of commands and liberal use of gnu parallel to improve efficiency.
Is there any template I can follow, where I can slot in my commands and get things running quickly?
EDIT - The skeleton of pipeline goes as follows (As I'm not sure if I can put our inhouse pipeline in its entirety here) -
Bash code which loops through R1 and R2, aligns with BWA-mem2 and sorts the bam, then using gnu parallel, I essentially follow the steps as outlined in GATK Best Practices (looking to drop BQSR, but the steps remain) to obtain a gvcf file. The steps in Best Practices have been turned to functions, rather than each step being called sequentially.