From bfd13c5b3d5cab532db756b28cee9c0b5eabc9c1 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 14 Sep 2023 14:40:01 -0500 Subject: [PATCH] v0.5.4 in docs --- external-instructions.md | 6 +++--- internal-instructions.md | 2 +- nextflow.config | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/external-instructions.md b/external-instructions.md index ab5ab4f4..ab043180 100644 --- a/external-instructions.md +++ b/external-instructions.md @@ -65,7 +65,7 @@ nextflow run AlexsLemonade/scpca-nf \ ``` Where `` is the **relative** path to the [configuration file](#configuration-files) that you have setup and `` 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 \ -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 index af3b32a7..d08448ab 100644 --- 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 index 90b68274..d66753cd 100644 --- 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