--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/conf/profiles.config	Mon Dec 02 10:40:55 2024 -0500
@@ -0,0 +1,101 @@
+profiles {
+    
+    standard {
+        process.executor = 'local'
+        params.cores = 1
+        params.python_module = ""
+        params.mummer_module = ""
+        params.skesa_module = ""
+        params.bedtools_module = ""
+        params.mash_module = ""
+        params.bbtools_module = ""
+    }
+    
+    slurmHPC {
+        process.executor = 'slurm'
+        params.cores = 20
+        params.python_module = "/nfs/software/modules/python/3.8.1"
+        params.mummer_module = "/nfs/software/modules/mummer/4.0.0"
+        params.skesa_module = "/nfs/software/modules/skesa/2.5.0"
+        params.bedtools_module = "/nfs/sw/Modules/bedtools"
+        params.bbtools_module = "/nfs/software/modules/bbtools/38.94"
+        params.mash_module = "/nfs/software/modules/mash/2.3"
+        params.trim_name = "_contigs_skesa"
+    }
+    
+    slurmHPC_int {
+        process.executor = 'local'
+        params.cores = 20
+        params.python_module = "/nfs/software/modules/python/3.8.1"
+        params.mummer_module = "/nfs/software/modules/mummer/4.0.0"
+        params.skesa_module = "/nfs/software/modules/skesa/2.5.0"
+        params.bedtools_module = "/nfs/sw/Modules/bedtools"
+        params.bbtools_module = "/nfs/software/modules/bbtools/38.94"
+        params.mash_module = "/nfs/software/modules/mash/2.3"
+        params.trim_name = "_contigs_skesa"
+    }
+    
+    slurm_nm {
+        process.executor = 'slurm'
+        params.cores = 1
+        params.python_module = ""
+        params.mummer_module = ""
+        params.skesa_module = ""
+        params.bedtools_module = ""
+        params.bbtools_module = ""
+        params.mash_module = ""
+        params.trim_name = ""
+    }
+    
+    standard_conda {
+        conda.enabled = true
+        conda.cacheDir = "${projectDir}/CSP2_env"
+        process.conda = "${projectDir}/conf/CSP2.yaml"
+        
+        process.executor = 'local'
+        params.cores = 1
+        params.python_module = ""
+        params.mummer_module = ""
+        params.skesa_module = ""
+        params.bedtools_module = ""
+        params.bbtools_module = ""
+        params.mash_module = ""
+        params.trim_name = ""
+    }
+
+    slurm_conda {
+        conda.enabled = true
+        conda.cacheDir = "${projectDir}/CSP2_env"
+        process.conda = "${projectDir}/conf/CSP2.yaml"
+        
+        process.executor = 'slurm'
+        params.cores = 1
+        params.python_module = ""
+        params.mummer_module = ""
+        params.skesa_module = ""
+        params.bedtools_module = ""
+        params.bbtools_module = ""
+        params.mash_module = ""
+        params.trim_name = ""
+    }
+    
+    csp2_galaxy {
+        conda.enabled = true
+        conda.useMicromamba = true
+        conda.cacheDir = "${projectDir}/CSP2_env"
+        process.conda = "${projectDir}/conf/CSP2.yaml"
+        
+        process.queue = 'centriflaken'
+        executor.$slurm.exitReadTimeout = 120000
+
+        process.executor = 'slurm'
+        params.cores = 8
+        params.python_module = ""
+        params.mummer_module = ""
+        params.skesa_module = ""
+        params.bedtools_module = ""
+        params.bbtools_module = ""
+        params.mash_module = ""
+        params.trim_name = ""
+    }
+}