#!/usr/bin/env bash
# Bulk download script for GSE290625
# Generated from Yeo Lab Knowledgebase
# Total files: 8

OUTDIR=GSE290625
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- SRA run files ---
# Tip: use 'fasterq-dump' from SRA Toolkit for FASTQ conversion
#      with optional renaming to original submitted FASTQ names.
# Set to 1 to rename SRR outputs (e.g. SRR_1.fastq.gz -> sample_R1.fastq.gz)
RENAME_SRA_TO_ORIGINAL=1

_compress_if_exists() {
  local stem="$1"
  if [ -f "${stem}.fastq" ]; then
    gzip -f "${stem}.fastq"
    echo "${stem}.fastq.gz"
    return 0
  fi
  if [ -f "${stem}.fq" ]; then
    gzip -f "${stem}.fq"
    echo "${stem}.fq.gz"
    return 0
  fi
  return 1
}

# Option A: Download via SRA Toolkit (recommended)
fasterq-dump --split-files SRR32510408
gz1="$(_compress_if_exists SRR32510408_1 || true)"
gz2="$(_compress_if_exists SRR32510408_2 || true)"
gzs="$(_compress_if_exists SRR32510408 || true)"

fasterq-dump --split-files SRR32510409
gz1="$(_compress_if_exists SRR32510409_1 || true)"
gz2="$(_compress_if_exists SRR32510409_2 || true)"
gzs="$(_compress_if_exists SRR32510409 || true)"

fasterq-dump --split-files SRR32510410
gz1="$(_compress_if_exists SRR32510410_1 || true)"
gz2="$(_compress_if_exists SRR32510410_2 || true)"
gzs="$(_compress_if_exists SRR32510410 || true)"

fasterq-dump --split-files SRR32510411
gz1="$(_compress_if_exists SRR32510411_1 || true)"
gz2="$(_compress_if_exists SRR32510411_2 || true)"
gzs="$(_compress_if_exists SRR32510411 || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32510/SRR32510408/SRR32510408.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32510/SRR32510409/SRR32510409.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32510/SRR32510410/SRR32510410.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32510/SRR32510411/SRR32510411.lite.1

# --- Additional data files ---
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32510/SRR32510408/SRR32510408.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32510/SRR32510409/SRR32510409.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32510/SRR32510410/SRR32510410.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32510/SRR32510411/SRR32510411.lite.1

echo "Download complete. Files saved to $OUTDIR"