diff Snakefile @ 32:13df910d0683 draft

Uploaded

--- a/Snakefile	Thu Nov 14 07:42:04 2019 +0000
+++ b/Snakefile	Tue Nov 19 03:02:23 2019 +0000
@@ -46,7 +46,7 @@
         raise cpe
 
 import re
-STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)')
+STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)')
 def remove_steps_files():
     #modify STEP and FILES
     #so we don't run download or unmapped steps
@@ -98,15 +98,6 @@
     #create fastq 2 if not paired
     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')))
-    #TODO may need to add additional symlinking for HISAT2 unmapped alignments
     return([run_acc, study_acc, genome, method])
 
 
@@ -185,10 +176,8 @@
     input: 
         config['output'] + '/{quad}.sjout.zst',
         config['output'] + '/{quad}.fastq_check.tsv.zst',
-        config['output'] + '/{quad}.bamcount_nonref.csv.zst',
         config['output'] + '/{quad}.bamcount_auc.tsv',
         config['output'] + '/{quad}.bamcount_frag.tsv',
-        config['output'] + '/{quad}.Chimeric.out.junction.zst',
         config['output'] + '/{quad}.all.exon_bw_count.zst',
         config['output'] + '/{quad}.unique.exon_bw_count.zst',
         config['output'] + '/{quad}.all.bw.zst',