ini pre_processing_config日至16S.cfg

Posted 2021-05-24

# OSD campaign year
YEAR="2015"
# OSD campaign month
MONTH="06"
# Kind of molecule
DNA="16S"
# When sequences where delivered
DELIVER="2016-03-11"
# Who is the provider
PROVIDER="lgc"
# Email to report results
MAIL="[e-mail]"
# 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"
# Set working directory
WD="/bioinf/projects/megx/scratch/osd"
# Output folders
ODIR="/bioinf/projects/osd/main/${YEAR}/${MONTH}/pre-processing/${DNA}"
# Set original raw data from sequencing provider
RAWWD="/bioinf/projects/osd/main/${YEAR}/${MONTH}/original-data/${PROVIDER}/${DNA}/${DELIVER}/RAW"
SILVANGSSUB="/bioinf/projects/osd/main/${YEAR}/${MONTH}/silvangs-submission"
# Adapters, primers and all others
# A tsv with the following columns: PoolName	SampleName	ForwardPrimerID	ForwardPrimerSequence	ReversePrimerID	ReversePrimerSequence	PoolIndexSequence	FragmentSize	campaign_name	site_id	year	campaign_date	artificial_number	dataset_name	primer_pair_name	InternalSampleName	remarks
#P1  RSD2015_001_16Snew	   515F-Y_01		ACAACCAGTTGTGYCAGCMGCCGCGGTAA	906R-jed_01		ACAACCAGTTCCGYCAATTYMTTTRAGTTT		ATCCGTCT		392		RSD		1	2015	2015-06		1			16S		alma-alma		RSD1_2015-06_1_16S_alma-alma						
TECHNICAL="/bioinf/projects/osd/main/${YEAR}/${MONTH}/original-data/lgc/${DNA}/${DELIVER}/OSD2015_2016-03-11_tagging-modified.tsv"
# Primer collection file
# A tsv with the following columns: PrimerName PrimerSequence
# Example: 515F  GTGCCAGCMGCCGCGGTAA
PCOLLECTION="/home/afernand/OSD-pre-test/OSD_primer_collection.txt"

# Programs and version used
FASTQCVER="0.11.4"
FASTQCEXE="/bioinf/software/fastqc/fastqc-${FASTQCVER}/fastqc"

# cutadapt
CAEXEC="/bioinf/software/anaconda/anaconda-2.1/bin/cutadapt"
CAVER="1.8-dev"
# If low read counts maybe you want to try without anchored adapters
ANCHOREDBS="FALSE"


# Select which software to use: trimmomatic or bbduk
ADAPCLIP="bbduk"
QUALTRIM="bbduk"
TRIMADAP="TruSeq3-PE.fa"
TRIMVER="0.32"
TRIMEXEC="/bioinf/software/trimmomatic/trimmomatic-${TRIMVER}/trimmomatic-${TRIMVER}.jar"
TRIMADAPDIR="/bioinf/software/trimmomatic/trimmomatic-${TRIMVER}/adapters/${TRIMADAP}"

BBMAPVER="35.14"
BBMAPEXEC="/bioinf/software/bbmap/bbmap-${BBMAPVER}"
BBDUKADAP="/bioinf/software/bbmap/bbmap-35.14/resources/adapters.fa"

# Merging software
PEAREXEC="/bioinf/software/pear/pear-0.9.5/bin/pear"
PEARVER="0.9.5"

# Parameters
TRIM_QS="33"
MINLEN="100"
WINLEN="4"
PHREDQUAL="20"