rliterman@0: profiles {
rliterman@0:     
rliterman@0:     standard {
rliterman@0:         process.executor = 'local'
rliterman@0:         params.cores = 1
rliterman@0:         params.python_module = ""
rliterman@0:         params.mummer_module = ""
rliterman@0:         params.skesa_module = ""
rliterman@0:         params.bedtools_module = ""
rliterman@0:         params.mash_module = ""
rliterman@0:         params.bbtools_module = ""
rliterman@0:     }
rliterman@0:     
rliterman@0:     slurmHPC {
rliterman@0:         process.executor = 'slurm'
rliterman@0:         params.cores = 20
rliterman@0:         params.python_module = "/nfs/software/modules/python/3.8.1"
rliterman@0:         params.mummer_module = "/nfs/software/modules/mummer/4.0.0"
rliterman@0:         params.skesa_module = "/nfs/software/modules/skesa/2.5.0"
rliterman@0:         params.bedtools_module = "/nfs/sw/Modules/bedtools"
rliterman@0:         params.bbtools_module = "/nfs/software/modules/bbtools/38.94"
rliterman@0:         params.mash_module = "/nfs/software/modules/mash/2.3"
rliterman@0:         params.trim_name = "_contigs_skesa"
rliterman@0:     }
rliterman@0:     
rliterman@0:     slurmHPC_int {
rliterman@0:         process.executor = 'local'
rliterman@0:         params.cores = 20
rliterman@0:         params.python_module = "/nfs/software/modules/python/3.8.1"
rliterman@0:         params.mummer_module = "/nfs/software/modules/mummer/4.0.0"
rliterman@0:         params.skesa_module = "/nfs/software/modules/skesa/2.5.0"
rliterman@0:         params.bedtools_module = "/nfs/sw/Modules/bedtools"
rliterman@0:         params.bbtools_module = "/nfs/software/modules/bbtools/38.94"
rliterman@0:         params.mash_module = "/nfs/software/modules/mash/2.3"
rliterman@0:         params.trim_name = "_contigs_skesa"
rliterman@0:     }
rliterman@0:     
rliterman@0:     slurm_nm {
rliterman@0:         process.executor = 'slurm'
rliterman@0:         params.cores = 1
rliterman@0:         params.python_module = ""
rliterman@0:         params.mummer_module = ""
rliterman@0:         params.skesa_module = ""
rliterman@0:         params.bedtools_module = ""
rliterman@0:         params.bbtools_module = ""
rliterman@0:         params.mash_module = ""
rliterman@0:         params.trim_name = ""
rliterman@0:     }
rliterman@0:     
rliterman@0:     standard_conda {
rliterman@0:         conda.enabled = true
rliterman@0:         conda.cacheDir = "${projectDir}/CSP2_env"
rliterman@0:         process.conda = "${projectDir}/conf/CSP2.yaml"
rliterman@0:         
rliterman@0:         process.executor = 'local'
rliterman@0:         params.cores = 1
rliterman@0:         params.python_module = ""
rliterman@0:         params.mummer_module = ""
rliterman@0:         params.skesa_module = ""
rliterman@0:         params.bedtools_module = ""
rliterman@0:         params.bbtools_module = ""
rliterman@0:         params.mash_module = ""
rliterman@0:         params.trim_name = ""
rliterman@0:     }
rliterman@0: 
rliterman@0:     slurm_conda {
rliterman@0:         conda.enabled = true
rliterman@0:         conda.cacheDir = "${projectDir}/CSP2_env"
rliterman@0:         process.conda = "${projectDir}/conf/CSP2.yaml"
rliterman@0:         
rliterman@0:         process.executor = 'slurm'
rliterman@0:         params.cores = 1
rliterman@0:         params.python_module = ""
rliterman@0:         params.mummer_module = ""
rliterman@0:         params.skesa_module = ""
rliterman@0:         params.bedtools_module = ""
rliterman@0:         params.bbtools_module = ""
rliterman@0:         params.mash_module = ""
rliterman@0:         params.trim_name = ""
rliterman@0:     }
rliterman@0:     
rliterman@36:     csp2_galaxy {
rliterman@0:         conda.enabled = true
rliterman@0:         conda.useMicromamba = true
rliterman@0:         conda.cacheDir = "${projectDir}/CSP2_env"
rliterman@0:         process.conda = "${projectDir}/conf/CSP2.yaml"
rliterman@0:         
rliterman@33:         process.queue = "ondemand-small"
rliterman@9: 
rliterman@0:         executor.$slurm.exitReadTimeout = 120000
rliterman@0: 
rliterman@0:         process.executor = 'slurm'
rliterman@28:         params.cores = 1
rliterman@0:         params.python_module = ""
rliterman@0:         params.mummer_module = ""
rliterman@0:         params.skesa_module = ""
rliterman@0:         params.bedtools_module = ""
rliterman@0:         params.bbtools_module = ""
rliterman@0:         params.mash_module = ""
rliterman@0:         params.trim_name = ""
rliterman@0:     }
rliterman@0: }