--- a/cfsan_centriflaken.xml	Sun Aug 28 00:37:10 2022 -0400
+++ b/cfsan_centriflaken.xml	Thu Jun 27 14:17:26 2024 -0400
@@ -1,13 +1,16 @@
-<tool id="cfsan_centriflaken" name="Centriflaken" version="0.2.0+galaxy0">
+<tool id="cfsan_centriflaken" name="Centriflaken" version="0.4.1+galaxy1">
     <description>An automated pipeline to generate a MAG of interest (E.coli or Salmonella) and perform serotyping.</description>
     <requirements>
-	<requirement type="package" version="22.04">nextflow</requirement>
+	<requirement type="package" version="24.04">nextflow</requirement>
 	<requirement type="package">graphviz</requirement>
     </requirements>    
     <version_command>nextflow -version</version_command>
     <command detect_errors="exit_code"><![CDATA[
 	mkdir -p cpipes-input || exit 1;
     pwd_path=\$(pwd);
+    time_stamp=\$(date +%Y-%m-%d-%s);
+    work_dir="\${pwd_path}/centriflaken_work_dir-"\${time_stamp};
+    mkdir -p \$work_dir || exit 1;
     #import re
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
 	    #for _, $unpaired in enumerate($input_read_type_cond.input):
@@ -34,7 +37,7 @@
 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
 	    #end for
     #end if
-	$__tool_directory__/0.4.0/cpipes
+	$__tool_directory__/0.4.2/cpipes
     --pipeline $input_read_type_cond.pipeline_cond.pipeline
     #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
         --fq_single_end true