manage accession2taxid file gz or not

subworkflows/00_databases.nf

@@ -64,8 +64,24 @@ workflow DATABASES {
                 ch_taxonomy = DOWNLOAD_TAXONOMY_DB.out.taxonomy
             }
             else if( params.taxonomy_dir ) {
-                ch_accession2taxid = Channel
-                    .fromPath(params.taxonomy_dir + '/prot.accession2taxid.FULL', checkIfExists: true)
+            	
+            	// Process accession2taxid file
+            	accession2taxid_gz = params.taxonomy_dir + '/prot.accession2taxid.FULL.gz'
+            	accession2taxid = file(params.taxonomy_dir + '/prot.accession2taxid.FULL')
+            	
+            	if (file(accession2taxid_gz).isFile()) {
+		        ch_accession2taxid = Channel.fromPath(accession2taxid_gz, checkIfExists: true)
+		        
+		}
+		else if (accession2taxid.isFile()) {
+			ch_accession2taxid = Channel.fromPath(accession2taxid, checkIfExists: true)
+		}
+		
+		else {
+			exit 1, "$accession2taxid[.gz] is expected but does not exist in the given --taxonomy_dir $params.taxonomy_dir."
+		}
+    		
+    		// Process taxdump dir
                 ch_taxdump = Channel
                     .fromPath(params.taxonomy_dir + '/new_taxdump', checkIfExists: true)
                 ch_taxonomy = ch_accession2taxid.combine(ch_taxdump)