--- a/cfsan_centriflaken.xml	Wed Jul 03 15:02:23 2024 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 03 15:16:39 2024 -0400
@@ -7,8 +7,7 @@
     <command detect_errors="exit_code"><![CDATA[
     time_stamp=\$(date +%Y-%m-%d-%s);
     work_dir="/galaxy/nf-work-dirs/centriflaken_work_dir-"\${time_stamp};
-    input_path=\$(pwd)/cpipes-input;
-    mkdir -p "\${work_dir}" || exit 1;
+    input_path=\$(pwd)"/cpipes-input";
     mkdir -p "\${input_path}" || exit 1;
     #import re
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
@@ -36,7 +35,7 @@
 	        ln -sf '$pair.reverse' "\${input_path}/$read_R2";
 	    #end for
     #end if
-	nextflow /galaxy/cfsan-centriflaken-db/0.4.2/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
@@ -60,7 +59,7 @@
         #end if
     #end if
 	--input \${input_path}
-	--output \${work_dir}/cpipes-output
+	--output cpipes-output
     --fq_suffix '${input_read_type_cond.fq_suffix}'
     #if ($fq_filter_by_len != ""):
         --fq_filter_by_len $fq_filter_by_len
@@ -71,11 +70,9 @@
     #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
         --seqkit_rmdup_run true
     #end if
-    -work-dir \${work_dir}
 	-profile gxkubernetes;
-    mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' || exit 1;
-    mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs > /dev/null 2>&1 || exit 1;
-    rm -rf "\${work_dir}/cpipes-output" || exit 1;
+    mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' || exit 1;
+    mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs || exit 1;
     ]]></command>
     <inputs>
         <conditional name="input_read_type_cond">