runPipeline_snATAC_fastq.pbs

#!/bin/bash
#PBS -q home-epigen
#PBS -N snATAC_processing
#PBS -l nodes=1:ppn=16
#PBS -l walltime=24:00:00
#PBS -V
#PBS -m abe
#PBS -A epigen-group

#source activate bds_atac

WORKDIR="/oasis/tscc/scratch/$(whoami)/outputs_snATAC/"
FASTQDIR="/projects/ps-epigen/seqdata/"

# select libs 
samplenames=(`cat $samples`)
INPREFIX=${samplenames[${PBS_ARRAYID}*2]} #index start from 0
GENOME=${samplenames[${PBS_ARRAYID}*2+1]}
OUTDIR="${WORKDIR}${INPREFIX}"
mkdir -p $OUTDIR


fastq1="${FASTQDIR}/${INPREFIX}_R1.fastq.gz"
fastq2="${FASTQDIR}/${INPREFIX}_R2.fastq.gz"
echo $fastq1
[[ ! -f $fastq1 ]] && { echo "fastq1 not found"; exit 0; }
[[ ! -f $fastq2 ]] && { echo "fastq2 not found"; exit 0; } 


############################################################
# runPipeline
############################################################
source activate /home/opoirion/prog/conda_env
export PATH=$PATH:/home/opoirion/go/local/bin/
export PICARDHOME=/projects/ps-epigen/software/miniconda3/envs/bds_atac/share/picard-2.18.2-0/

## set up genome and args
if [ $GENOME = 'hg19' ] || [ $GENOME = 'hg38' ]
then
    GENOME="male.hg19"
    BOWTIE_INDEX="/home/opoirion/data/ref_genomes/human/male.hg19/Bowtie2Index"
    BOWTIE_INDEX_NAME="male.hg19.fa"
    REFSEQ_PROMOTER="/home/opoirion/data/ref_genomes/human/male.hg19/male.hg19_all_genes_refseq_TSS_promoter_2000.bed"
    CONSEC_PROMOTER="/home/opoirion/data/ref_genomes/human/male.hg19/male.hg19.refSeq_promoter.bed"
elif [ $GENOME = 'mm10' ]
then
    BOWTIE_INDEX="/home/opoirion/data/ref_genomes/mouse/mm10/Bowtie2Index"
    BOWTIE_INDEX_NAME="mm10"    
    REFSEQ_PROMOTER="/home/opoirion/data/ref_genomes/mouse/mm10/mm10_all_genes_refseq_TSS_promoter_2000.bed"
    CONSEC_PROMOTER="/home/opoirion/data/ref_genomes/mouse/mm10/mm10_consecutive_promoters.bed"
fi


## run
python /home/opoirion/code/snATAC/snATAC_pipeline/pipeline.py \
       -output_name $INPREFIX \
       -output_path $WORKDIR \
       -fastq_R1 $fastq1 -fastq_R2 $fastq2 \
       -ref_genome $GENOME \
       -aligner_to_use bowtie2 \
       -threads_number 16 \
       -bowtie_index_path $BOWTIE_INDEX \
       -bowtie_index_name $BOWTIE_INDEX_NAME \
       -refseq_promoter_file $REFSEQ_PROMOTER \
       -consecutive_promoter_file $CONSEC_PROMOTER \
       -bam_bigwig_for_top_clustering True \
       -perform_chromVAR_analysis True \
       -compute_TSS_enrichment True \
       -format_output_for_webinterface True \
       -workflow_version v2 \
       -java /home/opoirion/prog/jdk-10.0.1/bin/java 
wait


# add .finished.txt tag
touch ${OUTDIR}/.finished.txt

# transfer results
rsync -azr ${WORKDIR}${INPREFIX} ~/data/outputs/snATAC/


# qsub -t 1-15%1 
# use -v genome to tell which genome to run