Resume

[Eldad Kdoshim]

Hi All,
Is there a log where I can understand why Nextflow did not use the cache?
I'm running a pipeline with 3 processes, i had a problem in the 3rd process script.
i've fixed it, run with resume <session_id> , and although the other two processes finished successfully, Nextflow ran them instead of using the cache 

any ideas?
Thanks,
Eldad 

[Paolo Di Tommaso]

Use the command line option -dump-hashes 

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[Eldad Kdoshim]

Thanks, Paolo,

We notice that the resume issue was because of the '.groupTuple()' operator, which already has some discussions about.

before the process that fails to resume we use a groupTuple operator on the channel:

sample_grouped_sorted_bam_files = sorted_bam_ch .groupTuple() // extract the key string from `GroupKey` .map {sample_id, read_group, output_bam -> tuple(sample_id.toString(), read_group, output_bam)}

we noticed that it causes non-determinism in the order of the keys:
in the initial run we see these logs:

root@ip-172-26-122-180:/opt/manager# cat /efs/projects/cbu-664-6/nf/.nextflow.log.1 | grep "GroupTuple dynamic size" Jun-29 07:44:56.628 [Actor Thread 10] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=s_arcanum_la2157 size=1 Jun-29 07:44:56.694 [Actor Thread 10] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=s_arcanum_la2389 size=1

but in the resume run we see :

[ec2-user@ip-172-26-127-225 ~]$ cat /efs/projects/cbu-664-6/nf/.nextflow.log | grep "GroupTuple dynamic size" Jun-29 07:35:10.809 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=s_arcanum_la2389 size=1 Jun-29 07:35:10.811 [Actor Thread 5] DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=s_arcanum_la2157 size=1

the key in our case is a GroupKey and seems that we need to define a custom sort to make it deterministicwe have tried:

sample_grouped_sorted_bam_files = sorted_bam_ch .groupTuple( sort: {it.toString()}) // extract the key string from `GroupKey` .map {sample_id, read_group, output_bam -> tuple(sample_id.toString(), read_group, output_bam)}

 but it doesn't help.
Can you point us to the right way to do this sorting? (by the key's value)

Thanks!

[drhp...@gmail.com]

Hi Eldad!

It might be a good idea to do the sort directly in the process itself like here. This means you won't have to always sort the channels before passing to the process if the module is to be re-used elsewhere.

Hope that helps!

Cheers,

Harshil

[Eldad Kdoshim]

Harshil, Thanks for the replay 

We don't need the sorting on the process, I want the resume to work - for that, I need the result of the groupTuple() to be sorted

my previous mail maybe wasn't clear (I wrote it in a marked down editor but on gmail it as a plain text):
after the first run I see in the log:

DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=s_arcanum_la2157 size=1 

DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=s_arcanum_la2389 size=1

but on the 2nd run with the -resume flag, it's the same lines but in different order 

DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=s_arcanum_la2389 size=1

DEBUG nextflow.extension.GroupTupleOp - GroupTuple dynamic size: key=s_arcanum_la2157 size=1

since the order is not kept, the resume mechanism not working the processes are running again instead of getting the result from the cache 

So we tried to sort with  

sorted_bam_ch.groupTuple( sort: {it.toString()}) 

but it doesn't seems to work. 
Sorted_bam_ch contains a tuple with 3 values, where the first value is the key, of type GroupKey (that is why we use toString()).

Thanks!

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