Add trimmomatic SE.

bio/trimmomatic/pe/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.bam", "--use-conda", "-F"])
+    subprocess.check_call(["snakemake", "trimmed/a.1.fastq.gz", "--use-conda", "-F"])

bio/trimmomatic/se/environment.yaml

@@ -0,0 +1,5 @@
+channels:
+  - bioconda
+  - r
+dependencies:
+  - trimmomatic ==0.36

bio/trimmomatic/se/meta.yaml

@@ -0,0 +1,4 @@
+name: "trimmomatic se"
+description: Trim single-end reads with trimmomatic.
+authors:
+  - Johannes Köster

bio/trimmomatic/se/test/Snakefile

@@ -0,0 +1,14 @@
+rule trimmomatic_pe:
+    input:
+        "reads/{sample}.fastq"
+    output:
+        "trimmed/{sample}.fastq.gz"
+    log:
+        "logs/trimmomatic/{sample}.log"
+    params:
+        # list of trimmers (see manual)
+        trimmer=["TRAILING:3"]
+        # optional parameters
+        extra=""
+    wrapper:
+        "master/bio/trimmomatic/se"

bio/trimmomatic/se/test/reads/a.fastq

@@ -0,0 +1,4 @@
+@1
+ACGGCAT
++
+!!!!!!!

bio/trimmomatic/se/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", "trimmed/a.fastq.gz", "--use-conda", "-F"])

bio/trimmomatic/se/wrapper.py

@@ -0,0 +1,16 @@
+__author__ = "Johannes Köster"
+__copyright__ = "Copyright 2016, Johannes Köster"
+__email__ = "koester@jimmy.harvard.edu"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+trimmer = " ".join(snakemake.params.trimmer)
+
+shell("trimmomatic SE {snakemake.params.extra} "
+      "{snakemake.input} {snakemake.output} "
+      "{trimmer} "
+      "{log}")