pindel2vcf.

bio/pindel/call/test/Snakefile

@@ -18,4 +18,4 @@ rule pindel:
         "logs/pindel.log"
     threads: 4
     wrapper:
-        "master/bio/pindel"
+        "master/bio/pindel/call"

bio/pindel/pindel2vcf/environment.yaml

@@ -0,0 +1,5 @@
+channels:
+  - bioconda
+  - r
+dependencies:
+  - pindel ==0.2.5b8

bio/pindel/pindel2vcf/meta.yaml

@@ -0,0 +1,4 @@
+name: pindel2vcf
+description: Convert pindel output to vcf.
+authors:
+  - Johannes Köster

bio/pindel/pindel2vcf/test/Snakefile

@@ -0,0 +1,12 @@
+rule pindel2vcf:
+    input:
+        ref="genome.fasta",
+        pindel="pindel/all_{type}"
+    output:
+        "calls/{type}.vcf"
+    params:
+        refname="hg38",  # mandatory, see pindel manual
+        refdate="20170110",  # mandatory, see pindel manual
+        extra=""  # extra params (except -f, -p, -R, -d, -v)
+    wrapper:
+        "master/bio/pindel/pindel2vcf"

bio/pindel/pindel2vcf/test/genome.fasta

@@ -0,0 +1 @@
+../../call/test/genome.fasta

bio/pindel/pindel2vcf/test/genome.fasta.fai

@@ -0,0 +1 @@
+../../call/test/genome.fasta.fai

bio/pindel/pindel2vcf/test_wrapper.py

@@ -0,0 +1,8 @@
+import subprocess
+import os
+
+def setup_module():
+    os.chdir(os.path.join(os.path.dirname(__file__), "test"))
+
+def test():
+    subprocess.check_call(["snakemake", "calls/deletions.vcf", "--use-conda", "-F"])

bio/pindel/pindel2vcf/wrapper.py

@@ -0,0 +1,12 @@
+__author__ = "Johannes Köster"
+__copyright__ = "Copyright 2016, Johannes Köster"
+__email__ = "koester@jimmy.harvard.edu"
+__license__ = "MIT"
+
+import os
+from snakemake.shell import shell
+
+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}")