So far, the way to deal with samples with no reads is to remove them from the configuration file after a first run of the pipeline and re-run from scratch.
This is a good waste of resource and time so need to be improved.
Also allow to keep all samples, even the one without reads, in the final results, and allow to track back where could the issue arose.
Fail is either due to pair-end or quality trimming steps (quality and trim), some samples could have no more read after certain step, so rather add a switch at the beginning of each array step to exit if no read available,
Let Illumina_/454_quality step to handle 0 read samples and remove them from further analyses
Add another check at beginning of OTU step
So far, the way to deal with samples with no reads is to remove them from the configuration file after a first run of the pipeline and re-run from scratch. This is a good waste of resource and time so need to be improved. Also allow to keep all samples, even the one without reads, in the final results, and allow to track back where could the issue arose.
Fail is either due to pair-end or quality trimming steps (quality and trim), some samples could have no more read after certain step, so rather add a switch at the beginning of each array step to exit if no read available, Let Illumina_/454_quality step to handle 0 read samples and remove them from further analyses Add another check at beginning of OTU step