pipeline halts when quast finds no min length contigs

[nf-core]

pipeline halts when quast finds no min length contigs

[d4straub]

That's a little strange that the file contains no contigs at all. On the long run, it might be best to investigate how that happens and than correct that issue.

For fixing this immediately, you can try running your command appending -c quast.config where quast.config contains:

process {
  withName: quast {
    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
  }
}

This should make the pipeline ignore the issue and move on.
edit: dont forget to add -resume as well, otherwise you restart from scratch!

[d4straub]

Revisiting this issue, the assembly was not good enough, no contig at all. Most likely the underlying data is insufficient. Nevertheless, it would be of advantage if the pipeline would than skip quast, raise a warning and skip all downstream steps for that sample/assembly.

[d4straub]

I am not sure whether that is still an issue. Because the pipeline is supposed to be for assembly, I think its fine when the pipeline fails when no contig can be assembled.
If this continues to be a concern, please re-open.