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fix sub R1 R2
authorPeter Amstutz <peter.amstutz@curoverse.com>
Wed, 2 Jul 2014 20:37:20 +0000 (16:37 -0400)
committerPeter Amstutz <peter.amstutz@curoverse.com>
Wed, 2 Jul 2014 20:37:20 +0000 (16:37 -0400)
crunch_scripts/arvados-bcbio-nextgen.py patch | blob | history

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
index 692ace3df8d14ba156cb6cf278e432e29a46935c..52817376562b5dbea8df5366a3ab964a896672a3 100755 (executable)
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -95,8 +95,8 @@ with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc",
 os.chdir(arvados.current_task().tmpdir)
 
 rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/gatk-variant.yaml", "project1",
-                         subst.do_substitution(p, "$(R1)"),
-                         subst.do_substitution(p, "$(R2)")])
+                         subst.do_substitution(p, "$(file $(R1))"),
+                         subst.do_substitution(p, "$(file $(R2))")])
 
 os.chdir("project1/work")