v0.5.4 in docs

AlexsLemonade · Sep 14, 2023 · bfd13c5 · bfd13c5
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diff --git a/external-instructions.md b/external-instructions.md
@@ -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.
@@ -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>
 ```
@@ -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:

diff --git a/internal-instructions.md b/internal-instructions.md
@@ -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

diff --git a/nextflow.config b/nextflow.config
@@ -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