How to have process continue even if one fails

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1

I have a workflow that basically has two steps:

ch_source = TRANSFER_DATA(ch_samplesheet,dbinfo,web_ca)
UPDATEDB(ch_source,dbinfo,web_ca)

I just ran it on a sample sheet with 16 entried, and two of those failed early on. The rest did the TRANSFER_DATA process successfully but did even get into the UPDATEDB process. What happens when one process fails on something? What happens to the rest? it seems to me that the rest just stopped after TRANSFER_DATA.

I am running this using the Seqera Platform

2

The default process.errorStrategy is to terminate the pipeline immediately, including any other running processes: Process reference — Nextflow documentation. You can change this behaviour to ignore in which case the workflow completes even if any instances fails. The workflow will also exit successfully in that case. If you want the workflow to still report an error, you should also set workflow.failOnIgnore = true. This will let the workflow get as far as possible before reporting an error. It’s best to read the directive entry to see which value works best in your case.

3

Thank you!

4

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