Changed default database location

Author: olabiyi

Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/main.nf

@@ -97,7 +97,7 @@ if (params.help) {
   println()
   println("Paths to existing databases and database links.")
   println("        --DB_ROOT [PATH]   FULL PATH to root directory where the databases will be downloaded if they don't exist.") 
-  println("                  Relative paths such as '~/' and '../' will fail, please don't use them. Default: ./Reference_DBs/ ")
+  println("                  Relative paths such as '~/' and '../' will fail, please don't use them. Default: ../Reference_DBs/ ")
   println("CAT database directory strings:")
   println("    The strings below will be added to the end of the --database.cat_db path arguement provided below.")
   println("         --cat_taxonomy_dir [PATH] CAT taxonomy database directory. Default: 2021-01-07_taxonomy/.")

Metagenomics/Illumina/Workflow_Documentation/SW_MGIllumina/workflow_code/nextflow.config

@@ -46,13 +46,7 @@ params {
     logs_dir                = "../Logs/"
     metadata_dir            = "../Metadata/" 
 
-    //************************* Database creation **********************************//
-    /* Root directory where the databases will be downloaded if they don't exist.
-    This should be provided as a full path (starting with '/').
-    Note that relative paths such as '~/' and '../' are not expanded
-    by nextflow's evaluation of files, so don't use that.
-    */ 
-    DB_ROOT = "${baseDir}/Reference_DBs"
+    //************************* Databases **********************************//
     database {
         CAT_DB_LINK      = "https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz"
         // Old link - https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz 
@@ -169,7 +163,13 @@ profiles {
 // Maximum number of jobs to submit in parallel
 executor.queueSize = 20
 
-
+/* 
+    Root directory where the databases will be downloaded if they don't exist.
+    This should be provided as a full path (starting with '/').
+    Note that relative paths such as '~/' and '../' are not expanded
+    by nextflow's evaluation of files, so don't use that.
+*/ 
+params.DB_ROOT = ("${baseDir}".split("/")[0..-2]).join('/') + "/Reference_DBs"
 
 // Mount Humann databases to their predefined locations in the Biobakery container being used
 if(params.database.chocophlan_dir == null ||