#!/usr/bin/env bash
# Bulk download script for GSE277161
# Generated from Yeo Lab Publications Database
# Total files: 81

OUTDIR="GSE277161"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE277nnn/GSE277161/suppl/GSE277161_RAW.tar" -O "GSE277161_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 "SRR30661879"
gz1="$(_compress_if_exists 'SRR30661879_1' || true)"
gz2="$(_compress_if_exists 'SRR30661879_2' || true)"
gzs="$(_compress_if_exists 'SRR30661879' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "ZC3H3-BGRSDLV03-46_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "ZC3H3-BGRSDLV03-46_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661880"
gz1="$(_compress_if_exists 'SRR30661880_1' || true)"
gz2="$(_compress_if_exists 'SRR30661880_2' || true)"
gzs="$(_compress_if_exists 'SRR30661880' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "ZC3H3-BGRSDLV03-45_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "ZC3H3-BGRSDLV03-45_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661881"
gz1="$(_compress_if_exists 'SRR30661881_1' || true)"
gz2="$(_compress_if_exists 'SRR30661881_2' || true)"
gzs="$(_compress_if_exists 'SRR30661881' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "ZC3H3-BGRSDLV03-48dox_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "ZC3H3-BGRSDLV03-48dox_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661882"
gz1="$(_compress_if_exists 'SRR30661882_1' || true)"
gz2="$(_compress_if_exists 'SRR30661882_2' || true)"
gzs="$(_compress_if_exists 'SRR30661882' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "ZC3H3-BGRSDLV03-47dox_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "ZC3H3-BGRSDLV03-47dox_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661883"
gz1="$(_compress_if_exists 'SRR30661883_1' || true)"
gz2="$(_compress_if_exists 'SRR30661883_2' || true)"
gzs="$(_compress_if_exists 'SRR30661883' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WBP4-BGRSDLV03-42_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WBP4-BGRSDLV03-42_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661884"
gz1="$(_compress_if_exists 'SRR30661884_1' || true)"
gz2="$(_compress_if_exists 'SRR30661884_2' || true)"
gzs="$(_compress_if_exists 'SRR30661884' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WBP4-BGRSDLV03-44dox_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WBP4-BGRSDLV03-44dox_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661885"
gz1="$(_compress_if_exists 'SRR30661885_1' || true)"
gz2="$(_compress_if_exists 'SRR30661885_2' || true)"
gzs="$(_compress_if_exists 'SRR30661885' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WBP4-BGRSDLV03-43dox_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WBP4-BGRSDLV03-43dox_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661886"
gz1="$(_compress_if_exists 'SRR30661886_1' || true)"
gz2="$(_compress_if_exists 'SRR30661886_2' || true)"
gzs="$(_compress_if_exists 'SRR30661886' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "RNF14-BGRSDLV03-33_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "RNF14-BGRSDLV03-33_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661887"
gz1="$(_compress_if_exists 'SRR30661887_1' || true)"
gz2="$(_compress_if_exists 'SRR30661887_2' || true)"
gzs="$(_compress_if_exists 'SRR30661887' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "RNF14-BGRSDLV03-36dox_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "RNF14-BGRSDLV03-36dox_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661888"
gz1="$(_compress_if_exists 'SRR30661888_1' || true)"
gz2="$(_compress_if_exists 'SRR30661888_2' || true)"
gzs="$(_compress_if_exists 'SRR30661888' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "RNF14-BGRSDLV03-35dox_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "RNF14-BGRSDLV03-35dox_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661889"
gz1="$(_compress_if_exists 'SRR30661889_1' || true)"
gz2="$(_compress_if_exists 'SRR30661889_2' || true)"
gzs="$(_compress_if_exists 'SRR30661889' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WBP4-BGRSDLV03-41_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WBP4-BGRSDLV03-41_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661890"
gz1="$(_compress_if_exists 'SRR30661890_1' || true)"
gz2="$(_compress_if_exists 'SRR30661890_2' || true)"
gzs="$(_compress_if_exists 'SRR30661890' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "RNF113A-BGRSDLV03-30_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "RNF113A-BGRSDLV03-30_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661891"
gz1="$(_compress_if_exists 'SRR30661891_1' || true)"
gz2="$(_compress_if_exists 'SRR30661891_2' || true)"
gzs="$(_compress_if_exists 'SRR30661891' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "RNF113A-BGRSDLV03-29_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "RNF113A-BGRSDLV03-29_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661892"
gz1="$(_compress_if_exists 'SRR30661892_1' || true)"
gz2="$(_compress_if_exists 'SRR30661892_2' || true)"
gzs="$(_compress_if_exists 'SRR30661892' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "RNF14-BGRSDLV03-34_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "RNF14-BGRSDLV03-34_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661893"
gz1="$(_compress_if_exists 'SRR30661893_1' || true)"
gz2="$(_compress_if_exists 'SRR30661893_2' || true)"
gzs="$(_compress_if_exists 'SRR30661893' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "RNF113A-BGRSDLV03-32dox_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "RNF113A-BGRSDLV03-32dox_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661894"
gz1="$(_compress_if_exists 'SRR30661894_1' || true)"
gz2="$(_compress_if_exists 'SRR30661894_2' || true)"
gzs="$(_compress_if_exists 'SRR30661894' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661895"
gz1="$(_compress_if_exists 'SRR30661895_1' || true)"
gz2="$(_compress_if_exists 'SRR30661895_2' || true)"
gzs="$(_compress_if_exists 'SRR30661895' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661896"
gz1="$(_compress_if_exists 'SRR30661896_1' || true)"
gz2="$(_compress_if_exists 'SRR30661896_2' || true)"
gzs="$(_compress_if_exists 'SRR30661896' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661897"
gz1="$(_compress_if_exists 'SRR30661897_1' || true)"
gz2="$(_compress_if_exists 'SRR30661897_2' || true)"
gzs="$(_compress_if_exists 'SRR30661897' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "RNF113A-BGRSDLV03-31dox_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "RNF113A-BGRSDLV03-31dox_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661898"
gz1="$(_compress_if_exists 'SRR30661898_1' || true)"
gz2="$(_compress_if_exists 'SRR30661898_2' || true)"
gzs="$(_compress_if_exists 'SRR30661898' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661899"
gz1="$(_compress_if_exists 'SRR30661899_1' || true)"
gz2="$(_compress_if_exists 'SRR30661899_2' || true)"
gzs="$(_compress_if_exists 'SRR30661899' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MBNL1-BGRSDLV03-26_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "MBNL1-BGRSDLV03-26_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661900"
gz1="$(_compress_if_exists 'SRR30661900_1' || true)"
gz2="$(_compress_if_exists 'SRR30661900_2' || true)"
gzs="$(_compress_if_exists 'SRR30661900' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MBNL1-BGRSDLV03-25_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "MBNL1-BGRSDLV03-25_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661901"
gz1="$(_compress_if_exists 'SRR30661901_1' || true)"
gz2="$(_compress_if_exists 'SRR30661901_2' || true)"
gzs="$(_compress_if_exists 'SRR30661901' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MBNL1-BGRSDLV03-28dox_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "MBNL1-BGRSDLV03-28dox_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661902"
gz1="$(_compress_if_exists 'SRR30661902_1' || true)"
gz2="$(_compress_if_exists 'SRR30661902_2' || true)"
gzs="$(_compress_if_exists 'SRR30661902' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MBNL1-BGRSDLV03-27dox_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "MBNL1-BGRSDLV03-27dox_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661903"
gz1="$(_compress_if_exists 'SRR30661903_1' || true)"
gz2="$(_compress_if_exists 'SRR30661903_2' || true)"
gzs="$(_compress_if_exists 'SRR30661903' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FUS-BGRSDLV03-18_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FUS-BGRSDLV03-18_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661904"
gz1="$(_compress_if_exists 'SRR30661904_1' || true)"
gz2="$(_compress_if_exists 'SRR30661904_2' || true)"
gzs="$(_compress_if_exists 'SRR30661904' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FUS-BGRSDLV03-17_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FUS-BGRSDLV03-17_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661905"
gz1="$(_compress_if_exists 'SRR30661905_1' || true)"
gz2="$(_compress_if_exists 'SRR30661905_2' || true)"
gzs="$(_compress_if_exists 'SRR30661905' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FUS-BGRSDLV03-20dox_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FUS-BGRSDLV03-20dox_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661906"
gz1="$(_compress_if_exists 'SRR30661906_1' || true)"
gz2="$(_compress_if_exists 'SRR30661906_2' || true)"
gzs="$(_compress_if_exists 'SRR30661906' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FUS-BGRSDLV03-19dox_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "FUS-BGRSDLV03-19dox_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661907"
gz1="$(_compress_if_exists 'SRR30661907_1' || true)"
gz2="$(_compress_if_exists 'SRR30661907_2' || true)"
gzs="$(_compress_if_exists 'SRR30661907' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "ERI2-BGRSDLV03-14_merged_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "ERI2-BGRSDLV03-14_merged_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661908"
gz1="$(_compress_if_exists 'SRR30661908_1' || true)"
gz2="$(_compress_if_exists 'SRR30661908_2' || true)"
gzs="$(_compress_if_exists 'SRR30661908' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "ERI2-BGRSDLV03-13_S13_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "ERI2-BGRSDLV03-13_S13_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661909"
gz1="$(_compress_if_exists 'SRR30661909_1' || true)"
gz2="$(_compress_if_exists 'SRR30661909_2' || true)"
gzs="$(_compress_if_exists 'SRR30661909' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "ERI2-BGRSDLV03-16dox_S16_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "ERI2-BGRSDLV03-16dox_S16_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661910"
gz1="$(_compress_if_exists 'SRR30661910_1' || true)"
gz2="$(_compress_if_exists 'SRR30661910_2' || true)"
gzs="$(_compress_if_exists 'SRR30661910' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "ERI2-BGRSDLV03-15dox_S15_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "ERI2-BGRSDLV03-15dox_S15_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661911"
gz1="$(_compress_if_exists 'SRR30661911_1' || true)"
gz2="$(_compress_if_exists 'SRR30661911_2' || true)"
gzs="$(_compress_if_exists 'SRR30661911' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "CPSF4-BGRSDLV03-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "CPSF4-BGRSDLV03-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661912"
gz1="$(_compress_if_exists 'SRR30661912_1' || true)"
gz2="$(_compress_if_exists 'SRR30661912_2' || true)"
gzs="$(_compress_if_exists 'SRR30661912' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "CPSF4-BGRSDLV03-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "CPSF4-BGRSDLV03-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661913"
gz1="$(_compress_if_exists 'SRR30661913_1' || true)"
gz2="$(_compress_if_exists 'SRR30661913_2' || true)"
gzs="$(_compress_if_exists 'SRR30661913' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "CPSF4-BGRSDLV03-12dox_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "CPSF4-BGRSDLV03-12dox_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661914"
gz1="$(_compress_if_exists 'SRR30661914_1' || true)"
gz2="$(_compress_if_exists 'SRR30661914_2' || true)"
gzs="$(_compress_if_exists 'SRR30661914' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "CPSF4-BGRSDLV03-11dox_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "CPSF4-BGRSDLV03-11dox_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661915"
gz1="$(_compress_if_exists 'SRR30661915_1' || true)"
gz2="$(_compress_if_exists 'SRR30661915_2' || true)"
gzs="$(_compress_if_exists 'SRR30661915' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "CNOT4-BGRSDLV03-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "CNOT4-BGRSDLV03-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661916"
gz1="$(_compress_if_exists 'SRR30661916_1' || true)"
gz2="$(_compress_if_exists 'SRR30661916_2' || true)"
gzs="$(_compress_if_exists 'SRR30661916' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "CNOT4-BGRSDLV03-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "CNOT4-BGRSDLV03-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661917"
gz1="$(_compress_if_exists 'SRR30661917_1' || true)"
gz2="$(_compress_if_exists 'SRR30661917_2' || true)"
gzs="$(_compress_if_exists 'SRR30661917' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "CNOT4-BGRSDLV03-8dox_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "CNOT4-BGRSDLV03-8dox_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi

fasterq-dump --split-files "SRR30661918"
gz1="$(_compress_if_exists 'SRR30661918_1' || true)"
gz2="$(_compress_if_exists 'SRR30661918_2' || true)"
gzs="$(_compress_if_exists 'SRR30661918' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "CNOT4-BGRSDLV03-7dox_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "CNOT4-BGRSDLV03-7dox_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661879/SRR30661879"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661880/SRR30661880"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661881/SRR30661881"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661882/SRR30661882"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661883/SRR30661883"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661884/SRR30661884"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661885/SRR30661885"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661886/SRR30661886"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661887/SRR30661887"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661888/SRR30661888"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661889/SRR30661889"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661890/SRR30661890"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661891/SRR30661891"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661892/SRR30661892"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661893/SRR30661893"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661894/SRR30661894"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661895/SRR30661895"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661896/SRR30661896"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661897/SRR30661897"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661898/SRR30661898"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661899/SRR30661899"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661900/SRR30661900"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661901/SRR30661901"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661902/SRR30661902"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661903/SRR30661903"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661904/SRR30661904"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661905/SRR30661905"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661906/SRR30661906"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661907/SRR30661907"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661908/SRR30661908"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661909/SRR30661909"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661910/SRR30661910"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661911/SRR30661911"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661912/SRR30661912"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661913/SRR30661913"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661914/SRR30661914"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661915/SRR30661915"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661916/SRR30661916"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661917/SRR30661917"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661918/SRR30661918"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661916/SRR30661916"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661915/SRR30661915"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661918/SRR30661918"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661917/SRR30661917"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661912/SRR30661912"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661914/SRR30661914"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661913/SRR30661913"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661911/SRR30661911"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661908/SRR30661908"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661907/SRR30661907"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661910/SRR30661910"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661909/SRR30661909"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661904/SRR30661904"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661903/SRR30661903"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661906/SRR30661906"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661905/SRR30661905"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661900/SRR30661900"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661899/SRR30661899"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661902/SRR30661902"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661901/SRR30661901"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661895/SRR30661895"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661894/SRR30661894"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661898/SRR30661898"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661896/SRR30661896"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661891/SRR30661891"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661890/SRR30661890"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661897/SRR30661897"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661893/SRR30661893"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661886/SRR30661886"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661892/SRR30661892"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661888/SRR30661888"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661887/SRR30661887"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661889/SRR30661889"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661883/SRR30661883"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661885/SRR30661885"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661884/SRR30661884"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661880/SRR30661880"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661879/SRR30661879"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661882/SRR30661882"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR30661881/SRR30661881"

echo "Download complete. Files saved to $OUTDIR"