For reasons outside my control, I have to fetch fastq files from sra on a Windows computer. Currently I have a list of SRRs in a file, and a batch cmd file:
for /F "tokens=*" %%X in (SRR_Acc_List.txt) do ( prefetch %%X && vdb-validate %%X && fastq-dump [options] %%X )
Which works I think, but I don't know if it will prevent the fastq-dump command if the vdb-validate function says the sra is corrupt. Does anyone know the exit status of vdb-validate when it completes but the validation failed?