#!/usr/bin/env bash
# Bulk download script for GSE130238
# Generated from Yeo Lab Publications Database
# Total files: 9

OUTDIR="GSE130238"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE130nnn/GSE130238/suppl/GSE130238_RAW.tar" -O "GSE130238_RAW.tar"

# --- 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 "SRR8948931"
gz1="$(_compress_if_exists 'SRR8948931_1' || true)"
gz2="$(_compress_if_exists 'SRR8948931_2' || true)"
gzs="$(_compress_if_exists 'SRR8948931' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "1M_cortical_organoids_R1.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "1M_cortical_organoids_R2.fastq.gz"
fi

fasterq-dump --split-files "SRR8948932"
gz1="$(_compress_if_exists 'SRR8948932_1' || true)"
gz2="$(_compress_if_exists 'SRR8948932_2' || true)"
gzs="$(_compress_if_exists 'SRR8948932' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "3M_cortical_organoids_R1.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "3M_cortical_organoids_R2.fastq.gz"
fi

fasterq-dump --split-files "SRR8948933"
gz1="$(_compress_if_exists 'SRR8948933_1' || true)"
gz2="$(_compress_if_exists 'SRR8948933_2' || true)"
gzs="$(_compress_if_exists 'SRR8948933' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "6M_cortical_organoids_R1.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "6M_cortical_organoids_R2.fastq.gz"
fi

fasterq-dump --split-files "SRR8948934"
gz1="$(_compress_if_exists 'SRR8948934_1' || true)"
gz2="$(_compress_if_exists 'SRR8948934_2' || true)"
gzs="$(_compress_if_exists 'SRR8948934' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "10M_cortical_organoids_R1.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "10M_cortical_organoids_R2.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8948931/SRR8948931"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8948932/SRR8948932"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8948933/SRR8948933"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8948934/SRR8948934"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8948934/SRR8948934"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8948931/SRR8948931"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8948932/SRR8948932"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8948933/SRR8948933"

echo "Download complete. Files saved to $OUTDIR"