Add pindel wrapper.

bio/pindel/environment.yaml

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+channels:
+  - bioconda
+  - r
+dependencies:
+  - pindel ==0.2.5b8

bio/pindel/meta.yaml

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+name: pindel
+description: Call variants with pindel.
+authors:
+  - Johannes Köster

bio/pindel/test/Snakefile

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+rule pindel:
+    input:
+        ref="genome.fasta",
+        # samples to call
+        samples=["mapped/a.bam"],
+        # bam configuration file, see http://gmt.genome.wustl.edu/packages/pindel/quick-start.html
+        config="pindel_config.txt"
+    output:
+        "calls/pindel.vcf"
+    params:
+        ""  # optional parameters (except -i, -f, -o)
+    log:
+        "logs/pindel.log"
+    threads: 4
+    wrapper:
+        "master/bio/pindel"

bio/pindel/test/genome.fasta

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+>Sheila
+GCTAGCTCAGAAAAAAAAAA

bio/pindel/test/genome.fasta.fai

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+Sheila	20	8	20	21

bio/pindel/test/pindel_config.txt

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+mapped/a.bam	300	a

bio/pindel/test_wrapper.py

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

bio/pindel/wrapper.py

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+__author__ = "Johannes Köster"
+__copyright__ = "Copyright 2016, Johannes Köster"
+__email__ = "koester@jimmy.harvard.edu"
+__license__ = "MIT"
+
+import os
+from snakemake.shell import shell
+
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+prefix = os.path.dirname(snakemake.output[0])
+
+shell("pindel {params} -i {snakemake.input.conf} -f {snakemake.input.ref} -o {prefix} {log}")