nextflow.config

params {
    
    help = false
}

process {
    withName: 'FASTQC|FASTQC2' {
        container = 'docker://staphb/fastqc:0.11.9'
	cpus = 8
	memory = '16 GB'
    }

    withName:trimmomatic{
       container = 'docker://staphb/trimmomatic:0.39'
    }

    withName:bbtools{
       container = 'docker://staphb/bbtools:38.76'
    }

    withName:bwa_INDEX {
        container = 'docker://staphb/bwa:0.7.17'
    }

    withName:bwa_aln{
        container = 'docker://staphb/bwa:0.7.17'
    }

    withName:samtools_conv{
        container = 'staphb/samtools'
    }

    withName:samtools_sort{
        container = 'staphb/samtools'
    }

    withName:'samtools_index|samtools|unmapped_proc'{
        container = 'staphb/samtools'
    }

    withName:samtools_mpileup{
        container = 'staphb/samtools'
        container = 'staphb/ivar'
    }

    withName:'bwa_INDEX_each|bwa_aln_proc' {
        container = 'docker://staphb/bwa:0.7.17'
	cpus = 14
    }

    withName:bcftools_mpileup{
        container = 'staphb/bcftools'
    }

    withName:'scrub|scrub2' {
                         
        //container = 'ncbi/sra-human-scrubber'
	container = 'ncbi/sra-human-scrubber:latest'
    }
		  
    withName:kraken {

        container = 'staphb/kraken2'
	cpus = 20
        memory = 140.GB
    }

    withName:bracken {

        container ='docker://staphb/bracken:latest'
	cpus = 20
        memory = 140.GB
    }

    withName:skesa_asbl {
        container = 'staphb/skesa'
        cpus = 8
        memory = 40.GB
    }
    
    withName:'bowtie_INDEX_each|bowtie2_aln_proc' {
        container = 'staphb/bowtie2'

    }
    
    withName:pilon {
        container = 'staphb/pilon:1.24'
        memory =  32.GB
        cpus =  16   
    }

    withName:blast_search {
        container = 'staphb/blast'
    }

    withName:quast{
       container = 'docker://staphb/quast:5.0.2'
    }

    withName:readssum{
       container = 'docker://staphb/lyveset:1.1.4f'
    }

    withName:multiqc{
       container = 'docker://staphb/multiqc:1.8'
    }

    withName:readsproc{
       container = 'staphb/lyveset'          
    }
   // withName:ivar_cons{
   //    container = 'staphb/ivar'

   // }

}

apptainer {
    enabled = true
}

//apptainer.cacheDir = './'
apptainer.autoMounts = true