# HG changeset patch
# User kkonganti
# Date 1720026694 14400
# Node ID dcd41789fb614da2656e7175dee3804be5109cb2
# Parent  45ccd0403784e1c9cfe9f9438484708da80c2265
planemo upload

diff -r 45ccd0403784 -r dcd41789fb61 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 03 13:00:16 2024 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 03 13:11:34 2024 -0400
@@ -38,7 +38,6 @@
     #end if
 	nextflow /galaxy/cfsan-centriflaken-db/0.4.2/cpipes
     --pipeline $input_read_type_cond.pipeline_cond.pipeline
-    -work-dir \${work_dir}
     #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
         --fq_single_end true
         --flye_genome_size '${genome_size}'
@@ -72,6 +71,7 @@
     #if (str($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/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' > /dev/null 2>&1 || exit 1;
     mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs > /dev/null 2>&1 || exit 1;