# HG changeset patch
# User dereeper
# Date 1757447106 0
# Node ID a7390bf9ac225c4d898ba6a658c8a5125f5b52f8
# Parent  8918456081007cc859455419c5e3dc82ca7ae95f
Uploaded

diff -r 891845608100 -r a7390bf9ac22 PanExplorer.xml
--- a/PanExplorer.xml	Sun May 11 18:59:19 2025 +0000
+++ b/PanExplorer.xml	Tue Sep 09 19:45:06 2025 +0000
@@ -22,6 +22,7 @@
 
 touch $vcf;
 touch $vntr_matrix;
+touch $gfa_file;
 
 #if $software=="pgap"
     snakemake --cores 1 --config identity=$min_identity -s \$PANEX_PATH/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG >>$logfile 2>&1;
@@ -97,6 +98,7 @@
  <data from_work_dir="outputs/heaps.tsv" format="txt" name="heaps" label="Heaps law alpha"/>
  <data from_work_dir="outputs/heatmap.svg.complete.pdf.distance_matrix.txt" format="txt" name="distance_matrix" label="Accessory based distance matrix"/>
  <data from_work_dir="outputs/all_genomes.vcf" format="vcf" name="vcf" label="VCF file"/>
+ <data from_work_dir="outputs/pggb_out/all_genomes.fa.smooth.final.gfa" format="gfa1" name="gfa_file" label="GFA file"/>
  <data format="txt" name="logfile" label="Logfile"/>
  <data format="txt" name="roary_log" label="Roary Logfile"/>
 </outputs>