new nextflow config

nextflow.config

@@ -54,9 +54,57 @@ profiles {
 
   conda {
   	process{
-  		conda= "/opt/miniconda3/envs/bacterial_wgs_training/"
-  		withName:srst2_resistance {
-    		conda = "/opt/miniconda3/envs/srst2/"
+  		// conda= "/opt/miniconda3/envs/bacterial_wgs_training/"
+  		withName:makeBWAindex {
+    		conda = "/opt/miniconda3/envs/bwa/"
+  		}
+  		withName:fastqc {
+    		conda = "/opt/miniconda3/envs/fastqc/"
+  		}
+  		withName:trimming {
+    		conda = "/opt/miniconda3/envs/fastp/"
+  		}
+  		withName:bwa {
+    		conda = "/opt/miniconda3/envs/bwa/"
+  		}
+  		withName:samtools {
+    		conda = "/opt/miniconda3/envs/mapping/"
+  		}
+  		withName:bwa_mapped {
+    		conda = "/opt/miniconda3/envs/mapping/"
+  		}
+  		withName:picard {
+    		conda = "/opt/miniconda3/envs/mapping/"
+  		}
+  		withName:unicycler {
+    		conda = "/opt/miniconda3/envs/unicycler/"
+  		}
+  		withName:quast {
+    		conda = "/opt/miniconda3/envs/quast/"
+  		}
+  		withName:prokka {
+    		conda = "/opt/miniconda3/envs/prokka/"
+  		}
+  		withName:snippy {
+    		conda = "/opt/miniconda3/envs/samtools/"
+  		}
+  		withName:snippy_core {
+    		conda = "/opt/miniconda3/envs/samtools/"
+  		}
+  		withName:gubbins {
+    		conda = "/opt/miniconda3/envs/snippy/"
+  		}
+  		withName:iqtree {
+    		conda = "/opt/miniconda3/envs/iqtree/"
+  		}
+  		withName:scheme_evaluation {
+    		conda = "/opt/miniconda3/envs/taranis/"
+  		}
+  		withName:taranis {
+    		conda = "/opt/miniconda3/envs/taranis/"
+  		}
+  		withName:plasmidid {
+    		conda = "/opt/miniconda3/envs/plasmidid/"
   		}
   		withName:srst2_virulence {
     		conda = "/opt/miniconda3/envs/srst2/"
@@ -67,6 +115,24 @@ profiles {
   		withName:srst2_serogroup {
     		conda = "/opt/miniconda3/envs/srst2/"
   		}
+  		withName:srst2_resistance {
+    		conda = "/opt/miniconda3/envs/srst2/"
+  		}
+  		withName:multiqc_preprocessing {
+    		conda = "/opt/miniconda3/envs/multiqc/"
+  		}
+  		withName:multiqc_mapping {
+    		conda = "/opt/miniconda3/envs/multiqc/"
+  		}
+  		withName:multiqc_assembly {
+    		conda = "/opt/miniconda3/envs/multiqc/"
+  		}
+  		withName:multiqc_outbreakSNP {
+    		conda = "/opt/miniconda3/envs/multiqc/"
+  		}
+  		withName:multiqc_preprocessing {
+    		conda = "/opt/miniconda3/envs/multiqc/"
+  		}
     }
   }