diff Snakefile @ 35:e4dc3d0c31de draft

Uploaded

--- a/Snakefile	Tue Nov 19 05:44:09 2019 +0000
+++ b/Snakefile	Wed Nov 20 00:44:24 2019 +0000
@@ -46,7 +46,8 @@
         raise cpe
 
 import re
-STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)')
+#limit the outputs/steps to only 1) STAR called junctions 2) all reads per-base coverage (BigWigs) 3) all reads exon summarized coverage 4) AUC (for QC)
+STEPS_FILES_FILTER=re.compile(r'(unmapped)|(download)|(salmon)|(extract_jx)|(jx_bed)|(manifest)|(nonref)|(Chimeric)(fastq_check)|(frag)|(unique)')
 def remove_steps_files():
     #modify STEP and FILES
     #so we don't run download or unmapped steps
@@ -175,17 +176,17 @@
 rule make_galaxy_links:
     input: 
         config['output'] + '/{quad}.sjout.zst',
-        config['output'] + '/{quad}.fastq_check.tsv.zst',
+        #config['output'] + '/{quad}.fastq_check.tsv.zst',
         config['output'] + '/{quad}.bamcount_auc.tsv',
-        config['output'] + '/{quad}.bamcount_frag.tsv',
+        #config['output'] + '/{quad}.bamcount_frag.tsv',
         config['output'] + '/{quad}.all.exon_bw_count.zst',
-        config['output'] + '/{quad}.unique.exon_bw_count.zst',
+        #config['output'] + '/{quad}.unique.exon_bw_count.zst',
         config['output'] + '/{quad}.all.bw.zst',
-        config['output'] + '/{quad}.unique.bw.zst',
-        config['output'] + '/{quad}.fastq_check.log',
-        config['output'] + '/{quad}.align.log',
-        config['output'] + '/{quad}.sort.log',
-        config['output'] + '/{quad}.bamcount.log',
+        #config['output'] + '/{quad}.unique.bw.zst',
+        #config['output'] + '/{quad}.fastq_check.log',
+        #config['output'] + '/{quad}.align.log',
+        #config['output'] + '/{quad}.sort.log',
+        #config['output'] + '/{quad}.bamcount.log',
     output:
         config['output'] + '/{quad}.done'
     params: