# HG changeset patch
# User chrisw
# Date 1573717324 0
# Node ID de65ca58593076f1b044bb92e8d1ba9be8c1c6e0
# Parent  db147d9348fee31b36657a925a13d6583c6890af
Uploaded

diff -r db147d9348fe -r de65ca585930 Snakefile
--- a/Snakefile	Thu Nov 14 07:07:58 2019 +0000
+++ b/Snakefile	Thu Nov 14 07:42:04 2019 +0000
@@ -99,13 +99,13 @@
     if i == 2:
         open('%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 2), "w").close() 
     #create expected file structure for annotated exon bed file & reference index
-    ref = config['ref']
-    config['ref'] = os.path.abspath('.')
-    os.makedirs('%s/%s' % (config['ref'], genome))
-    os.symlink(ref, '%s/%s/star_idx' % (config['ref'], genome))
-    os.makedirs('%s/%s/gtf' % (config['ref'], genome))
-    os.symlink(config['exon_bed'], 'exons.tmp')
-    os.symlink('../../exons.tmp', '%s/%s/gtf/%s' % (config['ref'], genome, config.get('bw_bed', 'exons.bed')))
+    #ref = config['ref']
+    #config['ref'] = os.path.abspath('.')
+    #os.makedirs('%s/%s' % (config['ref'], genome))
+    #os.symlink(ref, '%s/%s/star_idx' % (config['ref'], genome))
+    #os.makedirs('%s/%s/gtf' % (config['ref'], genome))
+    #os.symlink(config['exon_bed'], 'exons.tmp')
+    #os.symlink('../../exons.tmp', '%s/%s/gtf/%s' % (config['ref'], genome, config.get('bw_bed', 'exons.bed')))
     #TODO may need to add additional symlinking for HISAT2 unmapped alignments
     return([run_acc, study_acc, genome, method])