Fixes.

snakemake · Feb 17, 2017 · 5211703 · 5211703
1 parent 5374fd6
commit 5211703
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/bio/pindel/__init__.py b/bio/pindel/__init__.py
diff --git a/bio/pindel/test/Snakefile b/bio/pindel/test/Snakefile
@@ -8,7 +8,9 @@ rule pindel:
     output:
         "calls/pindel.vcf"
     params:
-        ""  # optional parameters (except -i, -f, -o)
+        # prefix must be consistent with output files
+        prefix="calls/pindel",
+        extra=""  # optional parameters (except -i, -f, -o)
     log:
         "logs/pindel.log"
     threads: 4

diff --git a/bio/pindel/wrapper.py b/bio/pindel/wrapper.py
@@ -6,8 +6,7 @@
 import os
 from snakemake.shell import shell
 
-
+extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
-prefix = os.path.dirname(snakemake.output[0])
 
-shell("pindel {snakemake.params} -i {snakemake.input.config} -f {snakemake.input.ref} -o {prefix} {log}")
+shell("pindel {snakemake.params.extra} -i {snakemake.input.config} -f {snakemake.input.ref} -o {snakemake.params.prefix} {log}")