Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update version number in config and docs #458

Merged
merged 1 commit into from
Sep 14, 2023
Merged

Update version number in config and docs #458

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions external-instructions.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ nextflow run AlexsLemonade/scpca-nf \
```

Where `<path to config file>` is the **relative** path to the [configuration file](#configuration-files) that you have setup and `<name of profile>` is the name of the profile that you chose when [creating a profile](#setting-up-a-profile-in-the-configuration-file).
This command will pull the `scpca-nf` workflow directly from Github, using the `v0.5.3` version, and run it based on the settings in the configuration file that you have defined.
This command will pull the `scpca-nf` workflow directly from Github, using the `v0.5.4` version, and run it based on the settings in the configuration file that you have defined.

**Note:** `scpca-nf` is under active development.
Using the above command will run the workflow from the `main` branch of the workflow repository.
Expand All @@ -76,7 +76,7 @@ Released versions can be found on the [`scpca-nf` repo releases page](https://gi

```sh
nextflow run AlexsLemonade/scpca-nf \
-r v0.5.3 \
-r v0.5.4 \
-config <path to config file> \
-profile <name of profile>
```
Expand Down Expand Up @@ -280,7 +280,7 @@ If you will be analyzing spatial expression data, you will also need the Cell Ra

If your compute nodes do not have internet access, you will likely have to pre-pull the required container images as well.
When doing this, it is important to be sure that you also specify the revision (version tag) of the `scpca-nf` workflow that you are using.
For example, if you would run `nextflow run AlexsLemonade/scpca-nf -r v0.5.3`, then you will want to set `-r v0.5.3` for `get_refs.py` as well to be sure you have the correct containers.
For example, if you would run `nextflow run AlexsLemonade/scpca-nf -r v0.5.4`, then you will want to set `-r v0.5.4` for `get_refs.py` as well to be sure you have the correct containers.
By default, `get_refs.py` will download files and images associated with the latest release.

If your system uses Docker, you can add the `--docker` flag:
Expand Down
2 changes: 1 addition & 1 deletion internal-instructions.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ nextflow run AlexsLemonade/scpca-nf -profile ccdl,batch
When running the workflow for a project or group of samples that is ready to be released on ScPCA portal, please use the tag for the latest release:

```
nextflow run AlexsLemonade/scpca-nf -r v0.5.3 -profile ccdl,batch --project SCPCP000000
nextflow run AlexsLemonade/scpca-nf -r v0.5.4 -profile ccdl,batch --project SCPCP000000
```

### Processing example data
Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ manifest{
homePage = 'https://github.com/AlexsLemonade/scpca-nf'
mainScript = 'main.nf'
defaultBranch = 'main'
version = 'v0.5.3'
version = 'v0.5.4'
}

// global parameters for workflows
Expand Down