#!/bin/bash
set -euo pipefail
IFS=$'nt'

# Check for missing metadata file input
if [ -z ${1+x} ]; then
    echo "ERROR: missing input file; aborting."
    exit 1
fi

INPUT=$1

# Create / touch lists of series under processing / finished processing
touch processing.txt finished.txt

# Find GSE and SRR column numbers in metadata file
GSECOL=$(head -1 $INPUT | tr 't' 'n' | nl | grep GSE | cut -f 1 | tr -d ' ')
SRRCOL=$(head -1 $INPUT | tr 't' 'n' | nl | grep SRR | cut -f 1 | tr -d ' ')

# Main loop: for every unique GSE in metadata file
UNDER_PROCESSING=$(wc -l processing.txt | cut -d ' ' -f 1)
tail -n +2 $INPUT | cut -f $GSECOL | sort | uniq | while read GSE; do

    # Get all SRRs for current GSE
    RUNS=$(grep -w $GSE $INPUT | cut -f $SRRCOL)

    # Working directory
    WORKDIR=data/$CELL/$GSE

    # Skip if GSE is already finished or is currently being processed
    set +e
    if grep -wq $GSE processing.txt || grep -wq $GSE finished.txt; then
        continue
    fi
    set -e

    # Create directory structure
    mkdir -p $WORKDIR/01_fastq $WORKDIR/02_alignment $WORKDIR/03_expression

    # Start a maximum of 10 different series at once, then exit
    if [ $UNDER_PROCESSING -eq 10 ]; then
        echo "Started 10 different GSE series; stopping."
        echo ""
        exit 1
    else
        UNDER_PROCESSING=$(( $UNDER_PROCESSING + 1 ))
    fi

    # Queue downloads
    for SRR in $RUNS; do

        # Queue download
        sbatch --job-name $SRR.download
            --error $WORKDIR/01_fastq/slurm.download.fastq.$SRR.err
            --output $WORKDIR/01_fastq/slurm.download.fastq.$SRR.out
            --mail-type=NONE
            scripts/01_download_fastq.sh $GSE $SRR
                >> sbatch.download.ids 2>&1
    done

    # Queue alignment
    sbatch --job-name $GSE.alignment
        --error $WORKDIR/02_alignment/slurm.alignment.err
        --output $WORKDIR/02_alignment/slurm.alignment.out
        --mail-type=NONE
        --dependency=afterok:$(cat sbatch.download.ids | cut -d ' ' -f 4 | xargs | tr ' ' ':')
        scripts/02_alignment.sh $GSE
            > sbatch.alignment.id 2>&1

    rm sbatch.download.ids

    # Queue expression estimation
    sbatch --job-name $GSE.expression
        --error $WORKDIR/03_expression/slurm.expression.err
        --output $WORKDIR/03_expression/slurm.expression.out
        --mail-type=NONE
        --dependency=afterok:$(cat sbatch.alignment.id | cut -d ' ' -f 4)
        scripts/03_estimate_expression.sh $GSE
            > /dev/null

    rm sbatch.alignment.id

    # Add GSE to [processing.txt] file
    echo "$GSE" >> processing.txt
    echo "Queued pipeline for $GSE ($CELL); $UNDER_PROCESSING in queue."
done

#!/bin/bash -l
#SBATCH --account XXXXXXXX
#SBATCH --partition core
#SBATCH --ntasks 1
#SBATCH --job-name download.fastq
#SBATCH --time 15:00:00
#SBATCH --mail-user XXXXXXXXXXX
#SBATCH --mail-type=FAIL
#SBATCH --error log.download.fastq.err
#SBATCH --output log.download.fastq.out

# Get GSE and SRR IDs from input argument 1
GSE=$1
SRR=$2

# Working directory
WORKDIR=data/$CELL/$GSE

# Modules
module load bioinfo-tools sratools/2.8.0

# Download FASTQ files
fastq-dump --outdir $WORKDIR/01_fastq --gzip --skip-technical --split-files --readids --clip -v $SRR
    > $WORKDIR/01_fastq/log.download.fastq.$SRR.txt 2>&1

# Delete SRA file
if [ -f /proj/ncbi/sra/$SRR.sra ]; then
    rm /proj/ncbi/sra/$SRR.sra
fi