How do I change the version or update pgsc_calc?

Tip

It’s best to always use the most recent release, unless you’re trying to reproduce an old analysis

I’m running the workflow from nextflow directly

If you would like to use a specific version of pgsc_calc and are running the pipeline using our Github repository you can use some of the default nextflow parameters (see -r command docs).

To run a specific version:

$ nextflow run pgscatalog/pgsc_calc -profile <docker/singularity/conda> -r [version name, e.g. v2.0.0-alpha.5] ....

To run the latest version of a previously cloned repository you can use nextflow pull or add the -latest flag to a run command (see nextflow docs):

$ nextflow run pgscatalog/pgsc_calc -profile <docker/singularity/conda> -latest ....

I used git to clone the repository

By default the main branch contains the most recent release. You can use older releases with git:

$ cd path/to/pgsc_calc
$ git pull
$ git tag
...
v2.0.0-alpha.2
v2.0.0-alpha.3
v2.0.0-alpha.4
v2.0.0-alpha.5
$ git checkout v2.0.0-alpha.5

To switch back to the main branch:

$ cd path/to/pgsc_calc
$ git pull
$ git checkout main