createConfig.sh

#!/usr/bin/env bash

SOURCE=${BASH_SOURCE[0]}
DIR=$( dirname "$SOURCE" )
DIR_REALPATH=`realpath $DIR`

sampleID=$1
fastq=`realpath $2`
config=$3

STAR=`which STAR`
STAR_realpath=`realpath $STAR`

fastqc=`which fastqc`
fastqc_realpath=`realpath $fastqc`

samtools=`which samtools`
samtools_realpath=`realpath $samtools`

starcode=`which starcode`
starcode_realpath=`realpath $starcode`

cutadapt=`which cutadapt`
cutadapt_realpath=`realpath $cutadapt`

bedGraphToBigWig=`which bedGraphToBigWig`
bedGraphToBigWig_realpath=`realpath $bedGraphToBigWig`


echo "
# sample ids
sampleID : $sampleID

# InputFile:
file: $fastq

reference: GRCh38.p12
spikeIn: GRCm38.p6
prefix: Mus_musculus_

# compression type, gz or bz2
compression: gz

barcode_len: 10

barcode_linker: CTGTAGGCACCATCAAT

# star path
star : $STAR_realpath

# star index path
star_index : $DIR_REALPATH/data/GRCh38_p12_GRCm38_p6

star_params: $DIR_REALPATH/data/Parameters.in

annotation: $DIR_REALPATH/data/gencode.v28.vM18.primary_assembly.annotation.gff3

genome_fa: $DIR_REALPATH/data/GRCh38.p12.GRCm38.p6.primary_assembly.genome.fa

#FastQC
fastqc : $fastqc_realpath

# samtools
samtools : $samtools_realpath

starcode: $starcode_realpath

starcode_params: \"-d 0\"

cutadapt: $cutadapt_realpath

cutadapt_params: \"-a ATCTCGTATGCCGTCTTCTGCTTG -a AAAAAAAAAAGGGGGGGGGGGGGG -a GGGGGGGGGGGGGGGGGGGGGGG -e 0.2 -q 5 --max-n 0.9\"

bedGraphToBigWig : $bedGraphToBigWig

mask_bed: $DIR_REALPATH/data/masked.bed

star_params_unmapped: $DIR_REALPATH/data/Parameters.unmappedin
stats_bed: $DIR_REALPATH/data/maskingClasses.bed

mask_downstream: 300" > $config