Add fastq_screen conf template.

conf/fastq_screen.conf

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+# This is an example configuration file for FastQ Screen
+
+############################
+## Bowtie, Bowtie 2 or BWA #
+############################
+## If the Bowtie, Bowtie 2 or BWA binary is not in your PATH, you can set 
+## this value to tell the program where to find your chosen aligner.  Uncomment 
+## the relevant line below and set the appropriate location.  Please note, 
+## this path should INCLUDE the executable filename.
+
+#BOWTIE	/usr/local/bin/bowtie/bowtie
+#BOWTIE2 /usr/local/bowtie2/bowtie2
+#BWA /usr/local/bwa/bwa
+
+
+
+############################################
+## Bismark (for bisulfite sequencing only) #
+############################################
+## If the Bismark binary is not in your PATH then you can set this value to 
+## tell the program where to find it.  Uncomment the line below and set the 
+## appropriate location. Please note, this path should INCLUDE the executable 
+## filename.
+
+#BISMARK	/usr/local/bin/bismark/bismark
+
+
+
+############
+## Threads #
+############
+## Genome aligners can be made to run across multiple CPU cores to speed up 
+## searches.  Set this value to the number of cores you want for mapping reads.
+
+THREADS		32
+
+
+
+##############
+## DATABASES #
+##############
+## This section enables you to configure multiple genomes databases (aligner index 
+## files) to search against in your screen.  For each genome you need to provide a 
+## database name (which can't contain spaces) and the location of the aligner index 
+## files.
+##
+## The path to the index files SHOULD INCLUDE THE BASENAME of the index, e.g:
+## /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
+## Thus, the index files (Homo_sapiens.GRCh37.1.bt2, Homo_sapiens.GRCh37.2.bt2, etc.) 
+## are found in a folder named 'GRCh37'.
+##
+## If, for example, the Bowtie, Bowtie2 and BWA indices of a given genome reside in 
+## the SAME FOLDER, a SINLGE path may be provided to ALL the of indices.  The index 
+## used will be the one compatible with the chosen aligner (as specified using the 
+## --aligner flag).  
+##
+## The entries shown below are only suggested examples, you can add as many DATABASE 
+## sections as required, and you can comment out or remove as many of the existing 
+## entries as desired.  We suggest including genomes and sequences that may be sources 
+## of contamination either because they where run on your sequencer previously, or may 
+## have contaminated your sample during the library preparation step.
+##
+## Human - sequences available from
+## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/
+#DATABASE	Human	/data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
+##
+## Mouse - sequence available from
+## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/
+#DATABASE	Mouse	/data/public/Genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37
+##
+## Ecoli- sequence available from EMBL accession U00096.2
+#DATABASE	Ecoli	/data/public/Genomes/Ecoli/Ecoli
+##
+## PhiX - sequence available from Refseq accession NC_001422.1
+#DATABASE	PhiX	/data/public/Genomes/PhiX/phi_plus_SNPs
+##
+## Adapters - sequence derived from the FastQC contaminats file found at: www.bioinformatics.babraham.ac.uk/projects/fastqc
+#DATABASE	Adapters	/data/public/Genomes/Contaminants/Contaminants
+##
+## Vector - Sequence taken from the UniVec database
+## http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
+#DATABASE	Vectors		/data/public/Genomes/Vectors/Vectors
+
+DATABASE	Human	/cromwell_root/tmp/fastq_screen_reference/genome
+DATABASE	Mouse	/cromwell_root/tmp/fastq_screen_reference/mouse
+DATABASE	ERCC	/cromwell_root/tmp/fastq_screen_reference/ERCC
+DATABASE	EColi	/cromwell_root/tmp/fastq_screen_reference/ecoli
+DATABASE	Adapter	/cromwell_root/tmp/fastq_screen_reference/adapters
+DATABASE	Vector	/cromwell_root/tmp/fastq_screen_reference/vector
+DATABASE	rRNA	/cromwell_root/tmp/fastq_screen_reference/rRNARef
+DATABASE	Virus	/cromwell_root/tmp/fastq_screen_reference/viral
+DATABASE	Yeast	/cromwell_root/tmp/fastq_screen_reference/GCF_000146045.2_R64_genomic_modify
+DATABASE	Mitoch	/cromwell_root/tmp/fastq_screen_reference/Human_mitoch
+DATABASE	Phix	/cromwell_root/tmp/fastq_screen_reference/phix