Merge pull request #795 from AlexsLemonade/jashapiro/scpcatools0.4.1

Use scpcatools 0.4.1 images

config/containers.config

@@ -1,10 +1,10 @@
 // Docker container images
-SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpcatools:v0.4.0'
-SCPCATOOLS_SLIM_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-slim:v0.4.0'
-SCPCATOOLS_ANNDATA_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-anndata:v0.4.0'
-SCPCATOOLS_REPORTS_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-reports:v0.4.0'
-SCPCATOOLS_SEURAT_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-seurat:v0.4.0'
-SCPCATOOLS_SCVI_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-scvi:v0.4.0'
+SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpcatools:v0.4.1'
+SCPCATOOLS_SLIM_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-slim:v0.4.1'
+SCPCATOOLS_ANNDATA_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-anndata:v0.4.1'
+SCPCATOOLS_REPORTS_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-reports:v0.4.1'
+SCPCATOOLS_SEURAT_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-seurat:v0.4.1'
+SCPCATOOLS_SCVI_CONTAINER = 'ghcr.io/alexslemonade/scpcatools-scvi:v0.4.1'
 
 ALEVINFRY_CONTAINER = 'quay.io/biocontainers/alevin-fry:0.7.0--h9f5acd7_1'
 BCFTOOLS_CONTAINER = 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0'

external-instructions.md

@@ -86,12 +86,12 @@ Using the above command will run the workflow from the `main` branch of the work
 To update to the latest released version you can run `nextflow pull AlexsLemonade/scpca-nf` before the `nextflow run` command.
 
 To be sure that you are using a consistent version, you can specify use of a release tagged version of the workflow, set below with the `-r` flag.
-The command below will pull the `scpca-nf` workflow directly from Github using the `v0.8.4` version.
+The command below will pull the `scpca-nf` workflow directly from Github using the `v0.8.5` version.
 Released versions can be found on the [`scpca-nf` repository releases page](https://github.com/AlexsLemonade/scpca-nf/releases).
 
 ```sh
 nextflow run AlexsLemonade/scpca-nf \
-  -r v0.8.4 \
+  -r v0.8.5 \
   -config <path to config file>  \
   -profile <name of profile>
 ```
@@ -325,7 +325,7 @@ 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 v0.8.4`, then you will want to set `-r v0.8.4` 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 v0.8.5`, then you will want to set `-r v0.8.5` 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:

internal-instructions.md

@@ -87,7 +87,7 @@ Please refer to our [`CONTRIBUTING.md`](CONTRIBUTING.md#stub-workflows) for more
 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 v0.8.4 -profile ccdl,batch --project SCPCP000000
+nextflow run AlexsLemonade/scpca-nf -r v0.8.5 -profile ccdl,batch --project SCPCP000000
 ```
 
 ### Processing example data

nextflow.config

@@ -5,7 +5,7 @@ manifest {
   homePage = 'https://github.com/AlexsLemonade/scpca-nf'
   mainScript = 'main.nf'
   defaultBranch = 'main'
-  version = 'v0.8.4'
+  version = 'v0.8.5'
 }
 
 // global parameters for workflows