nf-core
Template update for nf-core/tools version 2.11
A quick pass through the merge conflicts when merging dev into nf-core-template-merge-3.3.1 resolving most conflicts except in main.nf and cutandrun.nf.
I commented out the merge markers with // TODO: handle this merge conflict so removing these comments should allow handling the merge conflicts again.
Otherwise just check out all other files from this branch except the two workflow files and handle them separately or use the branch as guideline on how to handle the different merge conflicts
[!WARNING] Newer version of the nf-core template is available.
Your pipeline is using an old version of the nf-core template: 3.3.1. Please update your pipeline to the latest version.
For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.
