Tophat pipeline

This is a finished tophat-stringtie-cuffmerge-cuffdiff-cummerbund pipeline.

src/rules/fastqProcessors/FastQC.rules

+"""
+@version: 0.1
+
+Create quality report of a FASTQ file, mostly copied from https://github.com/inodb/snakemake-workflows/blob/master/bio/ngs/rules/quality_control/fastqc.rules
+
+Required programs:
+* FastQC
+* imagemagick
+
+"""
+
+__author__ = "Jan van Haarst"
+__email__ = "jan.vanhaarst@wur.nl"
+
+rule fastqc:
+    message: """Create quality report of FASTQ file with FastQC"""
+    threads: 8
+    input:  "reads/{genome}/{sample}/{replicate}/{name}.fastq.gz"
+    output: "FASTQC/{genome}/{sample}/{replicate}/{name}_fastqc.zip"
+    shell: "fastqc --threads {threads} --outdir FASTQC/{wildcards.genome}/{wildcards.sample}/{wildcards.replicate} --noextract {input}"
+
+# TODO : create rule to combine images from zip into single image (montage)
+#rule fastqc_montage:
+#    message : """Create montage of all FASTQC images"""
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