# HG changeset patch
# User kkonganti
# Date 1720186274 14400
# Node ID 45900148ca9e55f9987bbb980c530d3532e17df3
# Parent  04f6ac8ca13c716da0e7f63e89deef66ee2c9531
planemo upload

diff -r 04f6ac8ca13c -r 45900148ca9e cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 03 15:16:39 2024 -0400
+++ b/cfsan_centriflaken.xml	Fri Jul 05 09:31:14 2024 -0400
@@ -5,8 +5,6 @@
     </requirements>    
     <version_command>nextflow -version</version_command>
     <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 "\${input_path}" || exit 1;
     #import re
@@ -71,8 +69,8 @@
         --seqkit_rmdup_run true
     #end if
 	-profile gxkubernetes;
-    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;
+    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">