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# OSD campaign year
YEAR=2015
# OSD campaign month
MONTH=06
# Kind of molecule
DNA=16S
# When sequences where delivered
DELIVER=2016-01-26
# Who is the provider
PROVIDER=lgc
# Email to report results
MAIL=afernand@mpi-bremen.de
# Has been cherry picked
CHERRY=FALSE
#Set analysis:
# For 16S: barcode-sorting or adapter-clipping or primer-clipping or read-merging or quality-trimming
# For shotgun: barcode-sorting or adapter-clipping or primer-clipping or read-merging or quality-trimming
# Set scripts location
EXEC=/home/afernand/SANDBOX/analysis/analysis-scripts/trunk/osd-analysis/osd-pre-processing/16S/2016/lgc/barcode-sorting
# Set working directory
WD=/bioinf/projects/megx/scratch/osd/barcode-sorting/${DNA}/${PROVIDER}/${DELIVER}/pools
# Output folders
ODIR=/bioinf/projects/osd/main/2014/06/pre-processing/${DNA}/barcode-sorting/${PROV}/${DEL}
# Set original raw data from sequencing provider
RAWWD=/bioinf/projects/osd/main/2015/06/original-data/${PROVIDER}/${DNA}/${DELIVER}
# Adapters, primers and all others
# A tsv with the following columns: PoolName	SampleName	ForwardPrimerID	ForwardPrimerSequence	ReversePrimerID	ReversePrimerSequence	PoolIndexSequence
# Example: P1	RSD2015_001_16Snew	515F-Y_01	ACAACCAGTTGTGYCAGCMGCCGCGGTAA	906R-jed_01	ACAACCAGTTCCGYCAATTYMTTTRAGTTT	ATCCGTCT			
TECHNICAL=
# Primer collection file
# A tsv with the following columns: PrimerName PrimerSequence
# Example: 515F  GTGCCAGCMGCCGCGGTAA
PCOLLECTION=

# Programs and versions used
FASTQCEXE=/bioinf/software/fastqc/fastqc-0.11.4/fastq
FASTQCVER=0.11.4

515F  GTGCCAGCMGCCGCGGTAA
515F-Y  GTGYCAGCMGCCGCGGTAA
515YF GTGYCAGCMGCCGCGGTAA
341F  CCTACGGGNGGCWGCAG
U341F CCTAYGGGRBGCASCAG
Eu565F  CCAGCASCYGCGGTAATTCC
B806R GGACTACNVGGGTWTCTAAT
806R  GGACTACNVGGGTWTCTAAT
926R  CCGYCAATTYMTTTRAGTTT
906R-jed  CCGYCAATTYMTTTRAGTTT
1061R CRRCACGAGCTGACGAC
785R  GACTACHVGGGTATCTAAKCC
U806R GGACTACNNGGGTATCTAAT
Eu981R  ACTTTCGTTCTTGATYRATGA