# HG changeset patch
# User kkonganti
# Date 1719582204 14400
# Node ID da35e8151369cebcb29d9a8b7995268e3a6a8c98
# Parent  345d0a16f02600cbc21c404f0da85f032088a5b0
"planemo upload"

diff -r 345d0a16f026 -r da35e8151369 0.4.2/workflows/conf/centriflaken_hy.config
--- a/0.4.2/workflows/conf/centriflaken_hy.config	Fri Jun 28 09:34:56 2024 -0400
+++ b/0.4.2/workflows/conf/centriflaken_hy.config	Fri Jun 28 09:43:24 2024 -0400
@@ -9,13 +9,13 @@
     seqkit_rmdup_D = false
     seqkit_rmdup_P = false
     seqkit_rmdup_i = false
-    centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
+    centrifuge_x = '/galaxy/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
     centrifuge_extract_bug = 'Escherichia coli'
     centrifuge_save_aligned = false
     centrifuge_save_unaligned = false
     centrifuge_out_fmt_sam = false
     centrifuge_ignore_quals = false
-    kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
+    kraken2_db = '/galaxy/cfsan-centriflaken-db/0/kraken2/standard-210914'
     kraken2_confidence = '0.0'
     kraken2_quick = false
     kraken2_use_mpa_style = false
@@ -62,7 +62,7 @@
     ectyper_perc_opcov = 95
     ectyper_perc_hpcov = 50
     serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
-    serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
+    serotypefinder_db = '/galaxy/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
     serotypefinder_min_cov = 0.80
     serotypefinder_min_threshold = 0.85
     serotypefinder_x = true
@@ -76,10 +76,10 @@
     mlst_mincov = 10
     mlst_minscore = 50
     amrfinderplus_run = false
-    amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
+    amrfinderplus_db = '/galaxy/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
     amrfinderplus_genes = true
     abricate_run = true
-    abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
+    abricate_datadir = '/galaxy/cfsan-centriflaken-db/0/abricate/1.0.1/db'
     abricate_minid = 90
     abricate_mincov = 80
     abricate_summary_run = true