nextflow.config

manifest {
        mainScript = 'main.nf'
        description = 'Pipeline for FA analysis'
}

includeConfig "${params.config ?: 'params.config'}"

// Adapt queue entries below to match your infrastructure. If unsure, simply comment them with '//'
// More details at: https://www.nextflow.io/docs/latest/config.html
// If your queue system does not have access to Internet, you will need to download container images in advance
// and replace it in the different container properties of the different processes

process{
        queue='biocore-el7,long-sl7,short-sl7'
        time='6h'
        cpus='4'
        memory='24G'
        scratch = false
        maxRetries = 2
        errorStrategy = 'retry'

        withLabel: blast {
                queue='biocore-el7,long-sl7'
                time='48h'
                cpus='8'
                container="ncbi/blast:2.12.0"
        }

        withLabel: diamond {
                queue='biocore-el7,long-sl7'
                time='48h'
                cpus='8'
                container="quay.io/biocontainers/diamond:0.9.30--h56fc30b_0"
        }

        withLabel: blastannotator {
                queue='biocore-el7,short-sl7'
                cpus='1'
                memory='8G'
        }

        withLabel: gffcheck {
                queue='biocore-el7,short-sl7'
                cpus='1'
                container="quay.io/biocontainers/agat:0.8.0--pl5262hdfd78af_0"
        }

        // Process skipped with 'skip_sigtarp = true' in params.config
        withLabel: sigtarp {
                queue='biocore-el7,short-sl7'
                // Modify container value below with the resulting image from: https://github.com/biocorecrg/sigtarp_docker
                container="/software/bi/biocore_tools/git/singularity/sigtarp/sigtarp-5.0b.sif"
        }

        // Process skipped with 'skip_cdSearch = true' in params.config
        withLabel: cdSearch {
                queue='biocore-el7,short-sl7'
                cpus='1'
                memory='8G'
        }

        withLabel: ipscan {
                queue='biocore-el7,long-sl7'
                time='48h'
                cpus='8'
                // Modify container value below with the resulting image from: https://github.com/biocorecrg/interproscan_docker
                container="biocorecrg/interproscan:5.54-87.0"
                maxRetries=3
        }

        withLabel: kofamscan {
                queue='biocore-el7,long-sl7'
                time='48h'
                cpus='8'
                container="quay.io/biocontainers/kofamscan:1.3.0--hdfd78af_2"
        }

        withLabel: upload {
                time='48h'
        }
}

process.container = "guigolab/fa-nf:0.4.0"
// Singularity preferred. If chosen docker, uncomment line below, comment singularity one and replace sif containers above accordingly
// docker.enabled = true
singularity.enabled = true
// Location where Singularity images are cached. baseDir refers to the location from where the pipeline is executed
singularity.cacheDir = "$baseDir/singularity"