# HG changeset patch
# User chrisw
# Date 1550091941 18000
# Node ID f2258de365eeadc7fed4fac6d82e9b53b6bd42ff
# Parent  af1f49e5242dd45e06c15cee54812a511d0e3efa
Uploaded

diff -r af1f49e5242d -r f2258de365ee Snakefile
--- 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 \