nextflow run main.nf --help
nextflow run main.nf --fasta 'data/*.fa' --db data/db.fasta --cores 4 --outdir results -profile conda
You can switch between execution using docker containers and conda environments via
-profile [docker|conda]
Use the --chunk n parameter to automatically split a Fasta file into multiple Fasta files each containing n
sequences. The chunked Fasta files will processed separately and, if possible, in parallel. The final output will be merged and is the same like no chunk parameter was used.