Fixes.

snakemake · Feb 17, 2017 · 800a4c4 · 800a4c4
1 parent 0ea111b
commit 800a4c4
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/bio/pindel/pindel2vcf/test/Snakefile b/bio/pindel/pindel2vcf/test/Snakefile
@@ -7,6 +7,8 @@ rule pindel2vcf:
     params:
         refname="hg38",  # mandatory, see pindel manual
         refdate="20170110",  # mandatory, see pindel manual
-        extra=""  # extra params (except -f, -p, -R, -d, -v)
+        extra=""  # extra params (except -r, -p, -R, -d, -v)
+    log:
+        "logs/pindel/pindel2vcf.{type}.log"
     wrapper:
         "master/bio/pindel/pindel2vcf"
diff --git a/bio/pindel/pindel2vcf/wrapper.py b/bio/pindel/pindel2vcf/wrapper.py
@@ -9,4 +9,4 @@
 extra = snakemake.params.get("extra", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
-shell("pindel2vcf {snakemake.params.extra} -p {snakemake.input.pindel} -f {snakemake.input.ref} -R {snakemake.params.refname} -d {snakemake.params.refdate} -v {snakemake.output[0]} {log}")
+shell("pindel2vcf {snakemake.params.extra} -p {snakemake.input.pindel} -r {snakemake.input.ref} -R {snakemake.params.refname} -d {snakemake.params.refdate} -v {snakemake.output[0]} {log}")