Closed alexblaessle closed 8 months ago
This is by design, as it alerts you to the fact that they don't exist. However, you can configure the error strategy to ignore them, if you like.
Yep, there isn't much we can do here other than what @Midnighter suggested. Do any of the sra-tools have an option to validate a set of ids without downloading them? If so, we could have a pre-validation step that catches and reports this earlier and maybe even cleans the ids up before trying to download.
Closing now but please feel free to re-open if anyone finds this and has any bright ideas.
Description of the bug
I am downloading GTEX from dbgap (25k samples) and for some samples I am getting this error, causing the pipeline to crash.
Is there a way to add an exception if a few fastqs are not available?
Command used and terminal output
Relevant files
No response
System information
Nextflow version 23.04.2 Hardware HPC Executor slurm Container engine: Singularity OS CentOS LinuxVersion
nf-core/fetchngs