Add a parameter to decide how to assemble organelles.
( values: 'reads', 'contigs', 'none' ; not enforced atm).
The configuration option needed to run until completion ignoring failures is not yet in the main release of nextflow.
I think setting workflow.failOnIgnore to false should be the solution to this in the end.
If it Mitohifi fails, this should allow you continue without issue, or alternatively, disable it first and run, and then try the organelle assembly at the end by changing the parameter. The rest should stay cached, until we implement the filtering step.
Add a parameter to decide how to assemble organelles. ( values: 'reads', 'contigs', 'none' ; not enforced atm).
The configuration option needed to run until completion ignoring failures is not yet in the main release of nextflow. I think setting
workflow.failOnIgnoreto false should be the solution to this in the end.If it Mitohifi fails, this should allow you continue without issue, or alternatively, disable it first and run, and then try the organelle assembly at the end by changing the parameter. The rest should stay cached, until we implement the filtering step.