untracked changes

Author: replikation

workflows/process/abricate_samtool_extracter.nf

@@ -6,9 +6,9 @@ process abricate_samtool_extracter {
       path("*.fa")
     script:
       """
-        samtools_clinker_parser.sh ${tabfile} ${params.searchterm} ${params.range}
+        samtools_clinker_parser.sh ${tabfile} "${params.searchterm}" ${params.range}
 
-        samtools faidx ${fasta}
+        samtools faidx ${fasta} --continue
 
         while read fastaheader; do    
                 samtools faidx ${fasta} "\$fastaheader" >> "\${fastaheader}".fa