Manual synchronisation

There are rare cases, when the synchronisation needs to be triggered manually, i.e. it was not executed during an nf-core/tools release on Github, or when you want to perform a targeted sync.

Note that automated PR system is only applicable to official nf-core pipelines, homemade pipelines based on nf-core standards/modules created with nf-core create have to be updated following this manual synchronisation procedure.

You can do so by running the nf-core sync command:

cd my_pipeline
git checkout dev # or your most up to date branch
nf-core sync -d .

Note that the sync command assumes that you have a branch called TEMPLATE, so you may need to pull this from the upstream nf-core repository if you are working on a fork:

git remote add upstream
git checkout --track upstream/TEMPLATE

Remember to go back to your dev branch as above before running nf-core sync.

Much of the merging process should then be the same as described above with the automated pull requests.

In case of manual synchronisation of a homemade pipeline and if you want to have a PR opened to your dev branch, you can use this nf-core sync template command:

nf-core sync \
   --dir [pipeline_dir]
   --from-branch dev \
   --pull-request \
   --username [GitHub_username] \
   --github-repository [GitHub_pipeline_URL]