Update docs for 0.4.1

README.md

@@ -5,7 +5,7 @@
 > submit an issue.
 >
 > If interested in using the pipeline, feel free to check out its current
-> [documentation](https://zjnolen.github.io/PopGLen/v0.4.0/).
+> [documentation](https://zjnolen.github.io/PopGLen/v0.4.1/).
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14035397.svg)](https://doi.org/10.5281/zenodo.14035397)
 
@@ -31,11 +31,11 @@ GenErode, nf-core/eager, or your own custom processing).
 ## Documentation
 
 The main documentation for the pipeline is
-[here](https://zjnolen.github.io/PopGLen/v0.4.0/), with a broad summary of
+[here](https://zjnolen.github.io/PopGLen/v0.4.1/), with a broad summary of
 features reported in this README.
 
 Included in this documentation is a
-[tutorial](https://zjnolen.github.io/PopGLen/v0.4.0/tutorial/) which you can
+[tutorial](https://zjnolen.github.io/PopGLen/v0.4.1/tutorial/) which you can
 perform to become familiar with using PopGLen.
 
 ## Features

docs/config.md

@@ -90,7 +90,7 @@ A `units.tsv` where only BAMs are provided might look like this:
 `config.yaml` contains the configuration for the workflow, this is where you
 will put what analyses, filters, and options you want. Below I describe the
 configuration options. The `config.yaml`
-[distributed in the workflow repository](https://github.com/zjnolen/PopGLen/tree/v0.4.0/config)
+[distributed in the workflow repository](https://github.com/zjnolen/PopGLen/tree/v0.4.1/config)
 serves as a template and includes some 'default' parameters that may be good
 starting points for many users. If `--configfile` is not specified in the
 Snakemake command, the workflow will default to the file at

docs/getting-started.md

@@ -71,7 +71,7 @@ cd /path/to/work-dir
 And deploy the workflow, using the tag for the version you want to deploy:
 
 ```bash
-snakedeploy deploy-workflow https://github.com/zjnolen/PopGLen . --tag v0.4.0
+snakedeploy deploy-workflow https://github.com/zjnolen/PopGLen . --tag v0.4.1
 ```
 
 This will generate a simple Snakefile in a `workflow` folder that loads the
@@ -97,7 +97,7 @@ Move into the working directory (`PopGLen` or `work-dir-name` if you changed it)
 and checkout the version you would like to use:
 
 ```bash
-git checkout v0.4.0
+git checkout v0.4.1
 ```
 
 This can also be used to checkout specific branches or commits.

docs/resources.md

@@ -7,7 +7,7 @@ direct requests of memory when submitting SLURM jobs, instead always allocating
 workflow is to set `--default-resources mem_mb="XXXX * threads"` when running
 the Snakemake command, replacing `XXXX` with the RAM available per core on your
 HPC system in MB (in the case of ours, this was 6400). See the
-[profiles](https://github.com/zjnolen/PopGLen/tree/v0.4.0/profiles) in the
+[profiles](https://github.com/zjnolen/PopGLen/tree/v0.4.1/profiles) in the
 GitHub repository as an example.
 
 However, the default resources may not always work, your data may need more
@@ -19,7 +19,7 @@ in the workflow already.
 
 This is even better set up in a profile. PopGLen includes a default profile in
 the
-[profiles/default](https://github.com/zjnolen/PopGLen/tree/v0.4.0/profiles/default)
+[profiles/default](https://github.com/zjnolen/PopGLen/tree/v0.4.1/profiles/default)
 folder, which has all the rules already populated with the default resources
 already set. If you have downloaded the workflow via cloning the repository, all
 you need to do is change the values to match your needs (which may require

docs/tutorial.md

@@ -61,7 +61,7 @@ conda activate popglen
 Now, create a working directory for your project, deploy the workflow inside:
 
 ``` bash
-snakedeploy deploy-workflow https://github.com/zjnolen/PopGLen . --tag v0.4.0
+snakedeploy deploy-workflow https://github.com/zjnolen/PopGLen . --tag v0.4.1
 ```
 
 This will download a `workflow` and `config` folder containing a the workflow
@@ -96,7 +96,7 @@ tutorial data.
     cd popglen-tutorial
 
     # deploy the workflow in here
-    snakedeploy deploy-workflow https://github.com/zjnolen/PopGLen . --tag v0.4.0
+    snakedeploy deploy-workflow https://github.com/zjnolen/PopGLen . --tag v0.4.1
 
     # download the tutorial data
     wget -O popglen-tut-data.zip https://figshare.com/ndownloader/articles/27453978/versions/1