fetch_seqs.bat

@echo off
set "TOOL_PATH="/path/bin/fastq-dump.exe"
set "OUT_DIR=/path/Downloaded"
set "SRR_LIST=srr_list.txt"

if not exist "%TOOL_PATH%" (
    echo Error: fastq-dump not found at %TOOL_PATH%
    exit /b
)

if not exist "%SRR_LIST%" (
    echo Error: srr_list.txt not found in the current directory
    exit /b
)

for /F "tokens=*" %%s in (%SRR_LIST%) do (
    echo Downloading %%s...
    "%TOOL_PATH%" --split-files --gzip --outdir "%OUT_DIR%" %%s
    if %errorlevel% neq 0 (
        echo Failed to download %%s
    )
)
echo All downloads complete.