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When a run fails/is killed, and then resumed, sometimes endorspy is not ran at all, leading to endogenous information missing from the multiqc report.
Steps to reproduce
Start any run that includes endorspy, and kill the job before resuming the run. Even if endorspy has already run, it will not be picked up in the resumed run and will not appear in the multiqc report.
Expected behaviour
endorspy processes are cached normally and included in the output.
Log files
Have you provided the following extra information/files:
The command used to run the pipeline
The .nextflow.log file
The exact error:
System
Hardware:
Executor:
OS:
Version
Nextflow Installation
Version: 21.04.0.5552
Container engine
Engine: singularity
version: 3.7.1
Image tag: nfcore/eager:2.4.2
Additional context
The current output of the endorspy process is a tuple instead of a file channel. I have a feeling that might be causing the behaviour.
During lane/seqtype merge, we do a groupTuple, and for the laneseqtype metas, during this step these get converted into a nextflow object called 'ArrayBag'. It appears that for whatever reason (that we don't understand), something inside the ArrayBag objects changes between a cancelled/interupted run, causing the join to fail on these two elements.
The workaround is to replace the arraybag with a simpler object, e.g. string or integer.
Description of the bug
When a run fails/is killed, and then resumed, sometimes
endorspy
is not ran at all, leading to endogenous information missing from the multiqc report.Steps to reproduce
Start any run that includes endorspy, and kill the job before resuming the run. Even if endorspy has already run, it will not be picked up in the resumed run and will not appear in the multiqc report.
Expected behaviour
endorspy processes are cached normally and included in the output.
Log files
Have you provided the following extra information/files:
.nextflow.log
fileSystem
Nextflow Installation
Container engine
Additional context
The current output of the endorspy process is a tuple instead of a file channel. I have a feeling that might be causing the behaviour.
eager/main.nf
Line 1812 in 43a239b
The MQC output channel of another process for comparison:
eager/main.nf
Line 691 in 43a239b
In general, multiqc input channels are file channels, but there are cases where they are actually tuple channels. this should be fixed throughout.
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