Description of nextflow configuration parameters
| param | value type | description |
|---|---|---|
| inputFilePath | string | Path to input file |
| queryFilePath | path | Path to query fasta file |
| targetFilePath | path | Path to genome fasta file |
| outputDir | path | Path to dir where you would like results stored |
| queryChunkSize | int | Splits fasta into smaller fastas containing the queryChunkSize number of reads. |
| esd2esiMemoryLimit | int | esd2esi memory limit |
| fsmmemory | int | Exonerate memory limit |
| maxintron | int | Value for --maxintron parameter for exonerate |
-
Install Nextflow
curl https://get.nextflow.io | bash -
Run the script
nextflow run VEuPathDB/proteinToGenomeAlignment -with-trace -c <config_file> -r main