big_test_genotoul.config 2.6 KB
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process.executor = 'slurm'
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includeConfig 'singularity.config'
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singularity.runOptions = "-B /work/bank/ -B /bank -B /work2 -B /work -B /save -B /home -B /work/project"
process.queue = 'workq'
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process {


  // Process-specific resource requirements
  cpus = { 1 * task.attempt }
  memory = { 2.GB * task.attempt }

  errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
  maxRetries = 4
  maxErrors = '-1'

    withName: cutadapt {
            cpus = 8
            memory = { 4.GB * task.attempt }
    }
    withName: sickle {
            memory = { 2.GB * task.attempt }
    }
    withLabel: fastqc {
            cpus = 8
            memory = { 2.GB * task.attempt }
    }
    withName: multiqc {
            memory = { 8.GB * task.attempt }
    }
    withName: host_filter {
        memory = { 6.GB * task.attempt }
        time = '48h'
        cpus = 6
    }
    withName: index_db_kaiju {
        memory = { 200.GB * task.attempt }
        cpus = 6
    }
    withName: kaiju {
        memory = { 60.GB * task.attempt }
        cpus = 20
    }
    withName: kaiju_merge {
        memory = { 2.GB * task.attempt }
        cpus = 20
    }
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    withName: assembly {
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        memory = { 60.GB * task.attempt }
        cpus = 14
    }
    withName: quast {
        cpus = 3
        memory = { 8.GB * task.attempt }
    }
    withName: reads_deduplication {
        memory = { 4.GB * task.attempt }
    }
    withName: assembly_filter {
        memory = { 4.GB * task.attempt }
        cpus = 2
    }
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     withName: prokka {
        memory = { 45.GB * task.attempt }
        cpus = 8
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    }
    withName: rename_contigs_genes{
        memory = { 2.GB * task.attempt }
    }
    withLabel: cd_hit {
        memory = { 50.GB * task.attempt }
        cpus = 16
    }
    withName: quantification {
        memory = { 50.GB * task.attempt }
    }
    withName: quantification_table {
        memory = { 100.GB * task.attempt }
    }
    withName: diamond {
        cpus = 8
        memory = { 22.GB * task.attempt }
    }
    withName: get_software_versions {
        memory = { 1.GB * task.attempt }
    }
    withLabel: binning {
	    memory = { 5.GB * task.attempt }
	}
    withName: cat {
	    cpus = 8
        memory = { 16.GB * task.attempt }
	}
	withName: eggnog_mapper_db {
	    cpus = 2
        memory = { 2.GB * task.attempt }
	}
	withName: eggnog_mapper {
	    cpus = 4
        memory = { 20.GB * task.attempt }
	}
	withName: merge_quantif_and_functional_annot {
	    cpus = 1
        memory = { 50.GB * task.attempt }
	}
	withName: make_functional_annotation_tables {
	    cpus = 1
        memory = { 50.GB * task.attempt }
	}
}