Nextflow resume

[Lavi Bharath]

Hi,

Currently we are trying analyze hundreds of whole exome samples and we would like to understand how jobs are being cached when used in "-resume" mode.

Sometimes when the job fails, we try to increase the memory and restart the nf job. Job starts from the scratch in such incidents.

Does that mean touching nf file always mean rerun?

Would like to know if this can be avoided. Thanks.

Regards

Lavanya

[Paolo Di Tommaso]

Identify which is the first process that's not resumed and make sure all inputs are properly declared. Eventually post the code here.

p

--
You received this message because you are subscribed to the Google Groups "Nextflow" group.
To unsubscribe from this group and stop receiving emails from it, send an email to nextflow+u...@googlegroups.com.
Visit this group at https://groups.google.com/group/nextflow.
For more options, visit https://groups.google.com/d/optout.

[Lavi Bharath]

Thanks Paola for your response.

Actually I haven't changed any of my input or nextflow config.

I added 'maxRetries 3' to process number 2 and resumed the job. But jobs re-started from process number 1 on wards. One of my colleague also had the same issue. He just changed the memory setting resumed the jobs but the whole workflow restarted. 

Hence would like to know whether even resetting memory or maxretries setting will be considered as some changes and hence the workflow gets restarted? 

Thanks again for your time and help.

Regads

Lavanya

[Paolo Di Tommaso]

This should not happen. Please isolate the problem in a test case and share it.

Cheers, p

[Lavi Bharath]

Thanks for your reply Paola.

Most of my testing are on Aws batch with data on S3.

Let me  rephrase my question in order to understand better.

Nextflow will resume if any of the inputs change or an change in the command-line is updated in the workflow.

Is this true for both local as well aws batch setup? 

Thanks again for your valuable time.

[Paolo Di Tommaso]

The cache is computed at task level, this means that a task is re-executed if either an input or the command script change.

Even a file last-modified timestamp update is considered a modified file.

Hope it helps.

Cheers, 

Paolo (ending with o :))

[Lavi Bharath]

Great. Thanks for the explanation Paolo.

Sorry for misspelling your name :)