FlicAnderson
commented
2 years ago Issue riboviz/#467 blocks #466 (add flag for DSL 1).
Minimum current work required WITHOUT Upgrading Nextflow: specifying users install Nextflow version 20.04 specifically.
Work required WITH Upgrading Nextflow:
- update install docs about nextflow versioning
- check dependencies and update install docs
- update developer documentation to mention DSL choices
- add #466 fix to run riboviz using DSL 1
- check nextflow vignettes run with new version (after #466)
- run riboviz tests
- test with full-size datasets from example-datasets
- test and update the "Run on Eddie" documentation (potentially requires updated modules or other details changing)
- ? new riboviz version release! ?
-
? new test dataset release to match latest riboviz version ?
I may have missed some steps or things that might need changes/fixes or checking, but this is at least a minimum of the work needed...
@ewallace this issue (upgrading Nextflow) may/may not require a new riboviz version release, as depending on what we do with #466 (presuming that nothing else in riboviz is broken by upgrading Nextflow to the latest version), this may change prep-riboviz.nf by adding the nextflow.enable.dsl=1 line, or possibly just add a new environment option to set-riboviz-env.sh riboviz environment file which runs DSL1 by default. Perhaps the latter would be best for backwards compatibility?
Now riboviz is being run using Nextflow version 20.04.1. In the upcoming version release (22.04), the default language Nextflow it is going to use to run its scripts it's going to change and be DSL2. Therefore we need to add the -dsl1 flag in the command running Nextflow or include other options mentioned here. The problem is that Nextflow version 20.04.1 doesn't include the possibility of adding this flag, as we think it was implemented in version 20.07. This means we need to upgrade riboviz's Nextflow version in order to be able to include the flag.