Mercurial > repos > chrisw > monorail_test

changeset 14:f2258de365ee draft

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Uploaded
author chrisw
date Wed, 13 Feb 2019 16:05:41 -0500
parents af1f49e5242d
children 3fa68a0d59c5
files Snakefile
diffstat 1 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/Snakefile	Wed Feb 13 15:53:50 2019 -0500
+++ b/Snakefile	Wed Feb 13 16:05:41 2019 -0500
@@ -14,9 +14,13 @@
          'all.exon_bw_count.zst', 'unique.exon_bw_count.zst',
          'manifest']
 
+#get rid of the pesky warnings about current paths
+#and make sure we're not assuming any wrong relative paths
 import os
 config['output']=os.path.abspath(config['output'])
 config['temp']=os.path.abspath(config['temp'])
+config['exon_bed']=os.path.abspath(config['exon_bed'])
+config['ref']=os.path.abspath(config['ref'])
 
 import subprocess
 def run_command(cmd_args):
@@ -159,8 +163,6 @@
     input:
         bam=config['temp'] + '/{quad}-sorted.bam',
         bamidx=config['temp'] + '/{quad}-sorted.bam.bai',
-        #exe='/bamcount/bamcount',
-        exe='bamcount',
         bed=lambda wildcards: '%s/%s/gtf/%s' % (config['ref'], wildcards.quad.split('_')[2], config.get('bw_bed', 'exons.bed'))
     output:
         nonref=config['output'] + '/{quad}.bamcount_nonref.csv.zst',
@@ -179,7 +181,7 @@
     shell:
         """
         TMP={config[temp]}/{params.srr}_bamcount
-        {input.exe} {input.bam} \
+        bamcount {input.bam} \
             --threads {threads} \
             --coverage \
             --no-head \