#!/usr/bin/env bash
# Bulk download script for GSE117290
# Generated from Yeo Lab Publications Database
# Total files: 114

OUTDIR="GSE117290"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117290/suppl/GSE117290_RAW.tar" -O "GSE117290_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 "SRR11683564"
gz1="$(_compress_if_exists 'SRR11683564_1' || true)"
gz2="$(_compress_if_exists 'SRR11683564_2' || true)"
gzs="$(_compress_if_exists 'SRR11683564' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_CNOT7_R1_IN_S53_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683565"
gz1="$(_compress_if_exists 'SRR11683565_1' || true)"
gz2="$(_compress_if_exists 'SRR11683565_2' || true)"
gzs="$(_compress_if_exists 'SRR11683565' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_CNOT7_R1_IP_S55_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683566"
gz1="$(_compress_if_exists 'SRR11683566_1' || true)"
gz2="$(_compress_if_exists 'SRR11683566_2' || true)"
gzs="$(_compress_if_exists 'SRR11683566' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_CNOT7_R2_IN_S54_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683567"
gz1="$(_compress_if_exists 'SRR11683567_1' || true)"
gz2="$(_compress_if_exists 'SRR11683567_2' || true)"
gzs="$(_compress_if_exists 'SRR11683567' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_CNOT7_R2_IP_S56_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683568"
gz1="$(_compress_if_exists 'SRR11683568_1' || true)"
gz2="$(_compress_if_exists 'SRR11683568_2' || true)"
gzs="$(_compress_if_exists 'SRR11683568' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_AIMP1_R1_IN_S41_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683569"
gz1="$(_compress_if_exists 'SRR11683569_1' || true)"
gz2="$(_compress_if_exists 'SRR11683569_2' || true)"
gzs="$(_compress_if_exists 'SRR11683569' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_AIMP1_R1_IP_S43_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683570"
gz1="$(_compress_if_exists 'SRR11683570_1' || true)"
gz2="$(_compress_if_exists 'SRR11683570_2' || true)"
gzs="$(_compress_if_exists 'SRR11683570' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_AIMP1_R2_IN_S42_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683571"
gz1="$(_compress_if_exists 'SRR11683571_1' || true)"
gz2="$(_compress_if_exists 'SRR11683571_2' || true)"
gzs="$(_compress_if_exists 'SRR11683571' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_AIMP1_R2_IP_S44_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683572"
gz1="$(_compress_if_exists 'SRR11683572_1' || true)"
gz2="$(_compress_if_exists 'SRR11683572_2' || true)"
gzs="$(_compress_if_exists 'SRR11683572' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_MTDH_R1_IN_S33_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683573"
gz1="$(_compress_if_exists 'SRR11683573_1' || true)"
gz2="$(_compress_if_exists 'SRR11683573_2' || true)"
gzs="$(_compress_if_exists 'SRR11683573' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_MTDH_R1_IP_S35_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683574"
gz1="$(_compress_if_exists 'SRR11683574_1' || true)"
gz2="$(_compress_if_exists 'SRR11683574_2' || true)"
gzs="$(_compress_if_exists 'SRR11683574' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_MTDH_R2_IN_S34_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683575"
gz1="$(_compress_if_exists 'SRR11683575_1' || true)"
gz2="$(_compress_if_exists 'SRR11683575_2' || true)"
gzs="$(_compress_if_exists 'SRR11683575' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_MTDH_R2_IP_S36_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683576"
gz1="$(_compress_if_exists 'SRR11683576_1' || true)"
gz2="$(_compress_if_exists 'SRR11683576_2' || true)"
gzs="$(_compress_if_exists 'SRR11683576' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_UBAP2L_R1_IN_S7_L007_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683577"
gz1="$(_compress_if_exists 'SRR11683577_1' || true)"
gz2="$(_compress_if_exists 'SRR11683577_2' || true)"
gzs="$(_compress_if_exists 'SRR11683577' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_UBAP2L_R1_IP_S8_L007_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683578"
gz1="$(_compress_if_exists 'SRR11683578_1' || true)"
gz2="$(_compress_if_exists 'SRR11683578_2' || true)"
gzs="$(_compress_if_exists 'SRR11683578' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_UBAP2L_R2_IN_S9_L007_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683579"
gz1="$(_compress_if_exists 'SRR11683579_1' || true)"
gz2="$(_compress_if_exists 'SRR11683579_2' || true)"
gzs="$(_compress_if_exists 'SRR11683579' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_UBAP2L_R2_IP_S10_L007_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683580"
gz1="$(_compress_if_exists 'SRR11683580_1' || true)"
gz2="$(_compress_if_exists 'SRR11683580_2' || true)"
gzs="$(_compress_if_exists 'SRR11683580' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_CLK3_R1_IN_S29_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683581"
gz1="$(_compress_if_exists 'SRR11683581_1' || true)"
gz2="$(_compress_if_exists 'SRR11683581_2' || true)"
gzs="$(_compress_if_exists 'SRR11683581' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_CLK3_R1_IP_S31_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683582"
gz1="$(_compress_if_exists 'SRR11683582_1' || true)"
gz2="$(_compress_if_exists 'SRR11683582_2' || true)"
gzs="$(_compress_if_exists 'SRR11683582' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_CLK3_R2_IN_S30_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683583"
gz1="$(_compress_if_exists 'SRR11683583_1' || true)"
gz2="$(_compress_if_exists 'SRR11683583_2' || true)"
gzs="$(_compress_if_exists 'SRR11683583' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_CLK3_R2_IP_S32_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683584"
gz1="$(_compress_if_exists 'SRR11683584_1' || true)"
gz2="$(_compress_if_exists 'SRR11683584_2' || true)"
gzs="$(_compress_if_exists 'SRR11683584' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_DDX6_R1-IN_S5_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683585"
gz1="$(_compress_if_exists 'SRR11683585_1' || true)"
gz2="$(_compress_if_exists 'SRR11683585_2' || true)"
gzs="$(_compress_if_exists 'SRR11683585' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_DDx6_R1-IP_S7_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683586"
gz1="$(_compress_if_exists 'SRR11683586_1' || true)"
gz2="$(_compress_if_exists 'SRR11683586_2' || true)"
gzs="$(_compress_if_exists 'SRR11683586' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_DDx6_R2-IN_S6_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683587"
gz1="$(_compress_if_exists 'SRR11683587_1' || true)"
gz2="$(_compress_if_exists 'SRR11683587_2' || true)"
gzs="$(_compress_if_exists 'SRR11683587' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_DDX6_R2-IP_S8_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683588"
gz1="$(_compress_if_exists 'SRR11683588_1' || true)"
gz2="$(_compress_if_exists 'SRR11683588_2' || true)"
gzs="$(_compress_if_exists 'SRR11683588' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_MEX3C_R1-IN_S21_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683589"
gz1="$(_compress_if_exists 'SRR11683589_1' || true)"
gz2="$(_compress_if_exists 'SRR11683589_2' || true)"
gzs="$(_compress_if_exists 'SRR11683589' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_MEX3C_R1-IP_S23_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683590"
gz1="$(_compress_if_exists 'SRR11683590_1' || true)"
gz2="$(_compress_if_exists 'SRR11683590_2' || true)"
gzs="$(_compress_if_exists 'SRR11683590' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_MEX3C_R2-IN_S22_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683591"
gz1="$(_compress_if_exists 'SRR11683591_1' || true)"
gz2="$(_compress_if_exists 'SRR11683591_2' || true)"
gzs="$(_compress_if_exists 'SRR11683591' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_MEX3C_R2-IP_S24_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683592"
gz1="$(_compress_if_exists 'SRR11683592_1' || true)"
gz2="$(_compress_if_exists 'SRR11683592_2' || true)"
gzs="$(_compress_if_exists 'SRR11683592' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_PARN_R1-IN_S25_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683593"
gz1="$(_compress_if_exists 'SRR11683593_1' || true)"
gz2="$(_compress_if_exists 'SRR11683593_2' || true)"
gzs="$(_compress_if_exists 'SRR11683593' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_PARN_R1-IP_S27_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683594"
gz1="$(_compress_if_exists 'SRR11683594_1' || true)"
gz2="$(_compress_if_exists 'SRR11683594_2' || true)"
gzs="$(_compress_if_exists 'SRR11683594' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_PARN_R2-IN_S26_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683595"
gz1="$(_compress_if_exists 'SRR11683595_1' || true)"
gz2="$(_compress_if_exists 'SRR11683595_2' || true)"
gzs="$(_compress_if_exists 'SRR11683595' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_PARN_R2-IP_S28_L003_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683596"
gz1="$(_compress_if_exists 'SRR11683596_1' || true)"
gz2="$(_compress_if_exists 'SRR11683596_2' || true)"
gzs="$(_compress_if_exists 'SRR11683596' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_SNRPA_R1_IN_S45_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683597"
gz1="$(_compress_if_exists 'SRR11683597_1' || true)"
gz2="$(_compress_if_exists 'SRR11683597_2' || true)"
gzs="$(_compress_if_exists 'SRR11683597' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_SNRPA_R1_IP_S47_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683598"
gz1="$(_compress_if_exists 'SRR11683598_1' || true)"
gz2="$(_compress_if_exists 'SRR11683598_2' || true)"
gzs="$(_compress_if_exists 'SRR11683598' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_SNRPA_R2_IN_S46_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683599"
gz1="$(_compress_if_exists 'SRR11683599_1' || true)"
gz2="$(_compress_if_exists 'SRR11683599_2' || true)"
gzs="$(_compress_if_exists 'SRR11683599' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_SNRPA_R2_IP_S48_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683600"
gz1="$(_compress_if_exists 'SRR11683600_1' || true)"
gz2="$(_compress_if_exists 'SRR11683600_2' || true)"
gzs="$(_compress_if_exists 'SRR11683600' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_TBO2_R1-IN_S11_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683601"
gz1="$(_compress_if_exists 'SRR11683601_1' || true)"
gz2="$(_compress_if_exists 'SRR11683601_2' || true)"
gzs="$(_compress_if_exists 'SRR11683601' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_TBO2_R1-IP_S15_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683602"
gz1="$(_compress_if_exists 'SRR11683602_1' || true)"
gz2="$(_compress_if_exists 'SRR11683602_2' || true)"
gzs="$(_compress_if_exists 'SRR11683602' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_TBO2_R2-IN_S12_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683603"
gz1="$(_compress_if_exists 'SRR11683603_1' || true)"
gz2="$(_compress_if_exists 'SRR11683603_2' || true)"
gzs="$(_compress_if_exists 'SRR11683603' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_TBO2_R2-IP_S16_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683604"
gz1="$(_compress_if_exists 'SRR11683604_1' || true)"
gz2="$(_compress_if_exists 'SRR11683604_2' || true)"
gzs="$(_compress_if_exists 'SRR11683604' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_BOLL_R1_IN_S49_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683605"
gz1="$(_compress_if_exists 'SRR11683605_1' || true)"
gz2="$(_compress_if_exists 'SRR11683605_2' || true)"
gzs="$(_compress_if_exists 'SRR11683605' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_BOLL_R1_IP_S51_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683606"
gz1="$(_compress_if_exists 'SRR11683606_1' || true)"
gz2="$(_compress_if_exists 'SRR11683606_2' || true)"
gzs="$(_compress_if_exists 'SRR11683606' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_BOLL_R2_IN_S50_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683607"
gz1="$(_compress_if_exists 'SRR11683607_1' || true)"
gz2="$(_compress_if_exists 'SRR11683607_2' || true)"
gzs="$(_compress_if_exists 'SRR11683607' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_BOLL_R2_IP_S52_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683608"
gz1="$(_compress_if_exists 'SRR11683608_1' || true)"
gz2="$(_compress_if_exists 'SRR11683608_2' || true)"
gzs="$(_compress_if_exists 'SRR11683608' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_IFIT2_R1-IN_S9_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683609"
gz1="$(_compress_if_exists 'SRR11683609_1' || true)"
gz2="$(_compress_if_exists 'SRR11683609_2' || true)"
gzs="$(_compress_if_exists 'SRR11683609' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_IFIT2_R1-IP_S13_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683610"
gz1="$(_compress_if_exists 'SRR11683610_1' || true)"
gz2="$(_compress_if_exists 'SRR11683610_2' || true)"
gzs="$(_compress_if_exists 'SRR11683610' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_IFIT2_R2-IN_S10_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683611"
gz1="$(_compress_if_exists 'SRR11683611_1' || true)"
gz2="$(_compress_if_exists 'SRR11683611_2' || true)"
gzs="$(_compress_if_exists 'SRR11683611' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_IFIT2_R2-IP_S14_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683612"
gz1="$(_compress_if_exists 'SRR11683612_1' || true)"
gz2="$(_compress_if_exists 'SRR11683612_2' || true)"
gzs="$(_compress_if_exists 'SRR11683612' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_NANOS3_R1-IN_S17_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683613"
gz1="$(_compress_if_exists 'SRR11683613_1' || true)"
gz2="$(_compress_if_exists 'SRR11683613_2' || true)"
gzs="$(_compress_if_exists 'SRR11683613' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_NANOS3_R1-IP_S19_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683614"
gz1="$(_compress_if_exists 'SRR11683614_1' || true)"
gz2="$(_compress_if_exists 'SRR11683614_2' || true)"
gzs="$(_compress_if_exists 'SRR11683614' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_NANOS3_R2-IN_S18_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683615"
gz1="$(_compress_if_exists 'SRR11683615_1' || true)"
gz2="$(_compress_if_exists 'SRR11683615_2' || true)"
gzs="$(_compress_if_exists 'SRR11683615' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_NANOS3_R2-IP_S20_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683616"
gz1="$(_compress_if_exists 'SRR11683616_1' || true)"
gz2="$(_compress_if_exists 'SRR11683616_2' || true)"
gzs="$(_compress_if_exists 'SRR11683616' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_TOB1_R1_IN_S37_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683617"
gz1="$(_compress_if_exists 'SRR11683617_1' || true)"
gz2="$(_compress_if_exists 'SRR11683617_2' || true)"
gzs="$(_compress_if_exists 'SRR11683617' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_TOB1_R1_IP_S39_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683618"
gz1="$(_compress_if_exists 'SRR11683618_1' || true)"
gz2="$(_compress_if_exists 'SRR11683618_2' || true)"
gzs="$(_compress_if_exists 'SRR11683618' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_TOB1_R2_IN_S38_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11683619"
gz1="$(_compress_if_exists 'SRR11683619_1' || true)"
gz2="$(_compress_if_exists 'SRR11683619_2' || true)"
gzs="$(_compress_if_exists 'SRR11683619' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EC_TOB1_R2_IP_S40_L004_R1_001.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683564/SRR11683564"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683565/SRR11683565"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683566/SRR11683566"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683567/SRR11683567"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683568/SRR11683568"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683569/SRR11683569"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683570/SRR11683570"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683571/SRR11683571"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683572/SRR11683572"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683573/SRR11683573"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683574/SRR11683574"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683575/SRR11683575"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683576/SRR11683576"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683577/SRR11683577"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683578/SRR11683578"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683579/SRR11683579"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683580/SRR11683580"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683581/SRR11683581"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683582/SRR11683582"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683583/SRR11683583"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683584/SRR11683584"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683585/SRR11683585"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683586/SRR11683586"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683587/SRR11683587"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683588/SRR11683588"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683589/SRR11683589"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683590/SRR11683590"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683591/SRR11683591"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683592/SRR11683592"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683593/SRR11683593"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683594/SRR11683594"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683595/SRR11683595"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683596/SRR11683596"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683597/SRR11683597"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683598/SRR11683598"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683599/SRR11683599"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683600/SRR11683600"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683601/SRR11683601"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683602/SRR11683602"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683603/SRR11683603"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683604/SRR11683604"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683605/SRR11683605"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683606/SRR11683606"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683607/SRR11683607"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683608/SRR11683608"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683609/SRR11683609"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683610/SRR11683610"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683611/SRR11683611"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683612/SRR11683612"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683613/SRR11683613"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683614/SRR11683614"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683615/SRR11683615"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683616/SRR11683616"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683617/SRR11683617"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683618/SRR11683618"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683619/SRR11683619"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683568/SRR11683568"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683569/SRR11683569"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683570/SRR11683570"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683571/SRR11683571"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683604/SRR11683604"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683605/SRR11683605"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683606/SRR11683606"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683607/SRR11683607"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683580/SRR11683580"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683581/SRR11683581"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683582/SRR11683582"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683583/SRR11683583"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683564/SRR11683564"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683565/SRR11683565"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683566/SRR11683566"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683567/SRR11683567"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683584/SRR11683584"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683585/SRR11683585"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683586/SRR11683586"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683587/SRR11683587"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683608/SRR11683608"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683609/SRR11683609"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683610/SRR11683610"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683611/SRR11683611"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683588/SRR11683588"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683589/SRR11683589"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683590/SRR11683590"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683591/SRR11683591"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683572/SRR11683572"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683573/SRR11683573"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683574/SRR11683574"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683575/SRR11683575"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683612/SRR11683612"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683613/SRR11683613"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683614/SRR11683614"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683615/SRR11683615"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683592/SRR11683592"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683593/SRR11683593"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683594/SRR11683594"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683595/SRR11683595"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683596/SRR11683596"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683597/SRR11683597"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683598/SRR11683598"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683599/SRR11683599"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683600/SRR11683600"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683601/SRR11683601"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683602/SRR11683602"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683603/SRR11683603"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683616/SRR11683616"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683617/SRR11683617"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683618/SRR11683618"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683619/SRR11683619"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683576/SRR11683576"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683577/SRR11683577"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683578/SRR11683578"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11683579/SRR11683579"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR011/11683/SRR11683611/SRR11683611.lite.1"

echo "Download complete. Files saved to $OUTDIR"