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# PEPPRO configuration file for an PRO-seq pipeline based on pypiper
tools: # absolute paths to required tools
python: python
samtools: samtools
bedtools: bedtools
bowtie2: bowtie2
seqkit: seqkit
fastp: fastp
cutadapt: cutadapt
flash: flash
seqtk: seqtk
fastqpair: fastq_pair
# UCSC tools
bigWigCat: bigWigCat
wigToBigWig: wigToBigWig
# for PyPiper NGTSK
picard: ${PICARD}
# optional tools
fqdedup: fqdedup
fastx: fastx
seqoutbias: seqOutBias
# user configure
genome_config: ${REFGENIE}
adapters: null # Set to null to use default adapter file included in repository
parameters: # parameters passed to bioinformatic tools, subclassed by tool
# Adjust/Add/Remove parameters for individual tools here
bowtie2_pre: # Modify bowtie2 prealignment settings
params: ""
# pipeline default: -k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
# -k 1: report up to <1> alns per read; MAPQ not meaningful
# -D 20: give up extending after <20> failed extends in a row
# -R 3: for reads w/ repetitive seeds, try <3> sets of seeds
# -N 1: max # mismatches in seed alignment; can be 0 or 1
# -L 20: length of seed substrings; must be >3, <32
# -i S,1,0.50: interval between seed substrings w/r/t read len
bowtie2: # Modify bowtie2 primary genome alignment settings
params: ""
# pipeline default: --very-sensitive -X 2000
# --very-sensitive: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
# -X 2000: paired-end maximum fragment length
params: "-q 10"
# -q: skip alignments with MAPQ < 10.
precedence: # Set the precedence of default genomic features
params: "Enhancer, Promoter, Promoter Flanking Region, 5' UTR, 3' UTR, Exon, Intron"
# pipeline default: Enhancer, Promoter, Promoter Flanking Region, 5' UTR,
# 3' UTR, Exon, Intron
# These features are all present in the Refgenie feat_annotation asset.