# HG changeset patch
# User kkonganti
# Date 1657731830 14400
# Node ID 770ce74dfc47c797270fbadacab4834c81af1ef7
# Parent  29fec32b8f47f58526da697674c0aa755a2ee811
"planemo upload"

diff -r 29fec32b8f47 -r 770ce74dfc47 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 13 12:59:20 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 13:03:50 2022 -0400
@@ -54,8 +54,8 @@
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	--centrifuge_extract_bug '${centrifuge_extract_bug}'
 	-profile kondagac;
-    mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
-    mv './cpipes-output/${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;
     rm -rf ./cpipes-output || exit 1;
     rm -rf ./work || exit 1
     ]]></command>