Fix shell command

snakemake · Feb 19, 2017 · d09d461 · d09d461
1 parent 73f6404
commit d09d461
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/bio/star/align/test_wrapper.py b/bio/star/align/test_wrapper.py
@@ -5,4 +5,4 @@ def setup_module():
     os.chdir(os.path.join(os.path.dirname(__file__), "test"))
 
 def test():
-    subprocess.check_call(["snakemake", "mapped/a/Aligned.out.bam", "--use-conda", "-F"])
+    subprocess.check_call(["snakemake", "star/a/Aligned.out.bam", "--use-conda", "-F"])
diff --git a/bio/star/align/wrapper.py b/bio/star/align/wrapper.py
@@ -23,12 +23,13 @@
 
 
 shell(
-    "(STAR "
+    "STAR "
     "{snakemake.params.extra} "
     "--runThreadN {snakemake.threads} "
     "--genomeDir {snakemake.params.index} "
     "--readFilesIn {snakemake.input.sample} "
     "{readcmd} "
     "--outSAMtype BAM "
     "--outFileNamePrefix {outprefix} "
-    "--outStd Log")
+    "--outStd Log "
+    "{log}")