# HG changeset patch
# User kkonganti
# Date 1656529162 14400
# Node ID 0a65e6fde7b6dcb10bdc7cf652b6934a07cac7a9
# Parent  9c06429a2ffbe2becd9c1e203fbc5806d22b93b5
"planemo upload"

diff -r 9c06429a2ffb -r 0a65e6fde7b6 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jun 29 14:57:16 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jun 29 14:59:22 2022 -0400
@@ -15,6 +15,18 @@
     --pipeline $pipeline
     #if ($pipeline == "centriflaken"):
         --fq_single_end true
+        --flye_genome_size '${genome_size}'
+        #if ($long_read_platform == "nanopore_corr"):
+            --flye_nano_corr true --flye_nano_raw false
+        #elif ($long_read_platform == "nanopore_hq"):
+            --flye_nano_hq true --flye_nano_raw false
+        #elif ($long_read_platform == "pacbio_raw"):
+            --flye_pacbio_raw true --flye_nano_raw false
+        #elif ($long_read_platform == "pacbio_corr"):
+            --flye_pacbio_corr true --flye_nano_raw false
+        #elif ($long_read_platform == "pacbio_hifi"):
+            --flye_pacbio_hifi true --flye_nano_raw false
+        #end if
     #elif ($pipeline == "centriflaken_hy"):
         #if ($reads_lib_layout == "single"):
             --fq_single_end true
@@ -28,18 +40,6 @@
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	--centrifuge_extract_bug '${centrifuge_extract_bug}'
-	--flye_genome_size '${genome_size}'
-    #if ($long_read_platform == "nanopore_corr"):
-        --flye_nano_corr true --flye_nano_raw false
-    #elif ($long_read_platform == "nanopore_hq"):
-        --flye_nano_hq true --flye_nano_raw false
-    #elif ($long_read_platform == "pacbio_raw"):
-        --flye_pacbio_raw true --flye_nano_raw false
-    #elif ($long_read_platform == "pacbio_corr"):
-        --flye_pacbio_corr true --flye_nano_raw false
-    #elif ($long_read_platform == "pacbio_hifi"):
-        --flye_pacbio_hifi true --flye_nano_raw false
-    #end if
 	-profile $runtime_profile
     -resume;
     mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';