#!/bin/bash
#SBATCH --job-name=cwl_chip_seq
#SBATCH --output=/data/reddylab/Hazel/chipseq/KLJR_180920/processing/chip_seq/logs/OCI_JQ1res-se-%a.out
#SBATCH --mail-user=xa2@duke.edu
#SBATCH --mail-type=FAIL,END
#SBATCH --mem=24000
#SBATCH --cpus-per-task=16

export PATH="/data/reddylab/software/bin:$PATH"
export PATH="/data/reddylab/software/cwl/bin:$PATH"
export PATH="/data/reddylab/software/preseq_v2.0:$PATH"
export PATH="/data/reddylab/software/rsem-1.2.21/:$PATH"
export PATH="/data/reddylab/software/phantompeakqualtools-1.2/:$PATH"
export PATH="/data/reddylab/software/miniconda2/envs/cwl10/bin:$PATH"

module load bedtools2
module load fastqc
module load samtools

# For Fastqc
export DISPLAY=:0.0

# Make sure temporary files and folders are created in a specific folder
mkdir -p /data/reddylab/Hazel/chipseq/KLJR_180920/processing/chip_seq/tmpdirs/tmp-OCI_JQ1res-se-${SLURM_ARRAY_TASK_ID}-
export TMPDIR="/data/reddylab/Hazel/chipseq/KLJR_180920/processing/chip_seq/tmpdirs/tmp-OCI_JQ1res-se-${SLURM_ARRAY_TASK_ID}-"

cwltool --debug \
    --non-strict \
    --preserve-environment PATH \
    --preserve-environment DISPLAY \
    --preserve-environment TMPDIR \
    --outdir /data/reddylab/Hazel/chipseq/KLJR_180920/processing/chip_seq/OCI_JQ1res-se  \
    --no-container \
    /data/reddylab/software/cwl/GGR-cwl/v1.0/ChIP-seq_pipeline/pipeline-se.cwl \
    /data/reddylab/Hazel/chipseq/KLJR_180920/processing/chip_seq/jsons/chip_seq_download_metadata.OCI_JQ1res-se-${SLURM_ARRAY_TASK_ID}.json