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emo-bon / MetaGOflow

MGnify oriented implementation for the Marine Genomic Observatories oriented pipeline, developed in the framework of an EOSC-Life funded project
https://metagoflow.readthedocs.io
Apache License 2.0
7 stars 7 forks source link

change running scripts structure #26

Open jprmachado opened 1 year ago

jprmachado commented 1 year ago

This PR aims to create a structure in the shell scripts so is not require to comment and uncomment depending if is running toil or docker/singularity version.

If approved this PR this will have implications in the #24 and should be changed accordingly

The Toil script also solves one issue that we got initially that was Toil was not creating util directories (e.g. log)

hariszaf commented 1 year ago

Please do not merge this PR yet. I have made some changes on the run_wf.sh script under the ro-crate branch and I think it's better to first merge my branch, then you merge the develop on yours and then we merge this PR

hariszaf commented 1 year ago

Hi @jprmachado I tried to merge everything we ve done to the other branches here. Hope it works. However, please check this out, I have not run any tests with that. I will make the release without this branch for now and if it does work we integrate it once you say so! :) Thanks again!